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The Elegance of Complication?

by Bradford

On page 344 of Signature in the Cell Meyer makes note of the interdependence of functionality existing in cells. The cellular relationships between DNA, ATP and proteins have sometimes been dubbed as the chicken-egg dilemma for origin of life explanations. Chicken-egg causal pathways are common to designed outcomes. They signal a logical point at which intelligent input can be indentified. But is a chicken-egg scenario compelling either for design or deniers of it? Meyer does more than leave the issue hanging.

The most highlighted approach to resolving the chicken-egg conundrum is probably the RNA world explanation. Its enzymatic and information storage properties are said to have been sufficient by proponents of the RNA world. The RNA world hypothesis has been much explored both at Telic Thoughts and within many other sites, papers and books.

Proteins are needed to synthesize DNA and DNA is needed for protein synthesis. ATP, the primary energy currency of cells, is itself synthesized in a process involving proteins. Breakthroughs are often commended with the benefit of hindsight for their simplicity and elegance. Now that a resolution is right in front of you it can be akin to a why was that not seen before reaction. That no doubt would be the reaction of RNA world proponents but a realistic assessment of the approach reveals that an attempt to explain away a chicken-egg dilemma requires that we back end an added dilemma namely, the need to explain a transition to a protein world i.e. the cellular dynamics we actually observe.

When analyzing the orign of life we find a chicken-egg puzzle within a chicken-egg. While this type of thing is not unique to the origin of life the second chicken-egg is central to the RNA world as well as a core theme in Meyer's book. The origin of stored information in nucleic acids is not explained by RNA's dual enzyme/storage roles. Natural selection requires specifiable criteria which do not necessarily coincide with the outcome one is attempting to demonstrate. Information storage and transmission entails a convention by which sequenced elements are defined. The orign of that convention must be plausibly included within a more encompassing process. That process involves more than citing chemical affinity between some amino acids and anticodons.

The information storage found in DNA is sequence dependent. Take the sequencing of a functional gene and scramble the order of its amino acid coding codons as well as the stop codon and function is lost. Function is lost because a once biologically meaningful sequence is made nonsense. Functional information is lost even as content and chemical bonding remain constant.

Explaining the origin of functional sequencing requires more than a hypothesis which includes both enzymatic and storage physical material. Functional information is a consequence of sequential order as much as it is content. It has inherently conceptual properties. Alphabet soups, like their prebiotic counterparts, are unordered with respect to sequencing. Your very material lunch soup is not free.

This entry was posted on Tuesday, January 12th, 2010 at 9:55 am and is filed under Books, Origin of Life, Proteins, Random Stuff, RNA. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/the-elegance-of-complication/trackback/

170 Responses to “The Elegance of Complication?”

  1. Chicken and Egg Problem in Origin of Life « The Design Spectrum Says:
    January 12th, 2010 at 12:27 pm

    [...] 12, 2010 by PDS Both RJS at Jesus Creed and Bradford at Telic Thoughts have taken up the "chicken and egg" problem discussed in Signature in the Cell by [...]

    2. Pingback by Chicken and Egg Problem in Origin of Life « The Design Spectrum — January 12, 2010 @ 12:27 pm

  2. computerist Says:
    January 12th, 2010 at 4:26 pm

    Hi Bradford,

    Sorry, this is sort of off topic:

    To our resident Darwinian friends. Since you say "information is leaked from the environment", I would like to know a) exactly what this information is, in what "form" does it come in b) how much of it is being leaked c) when its leaked (context) d) how it applies to obtain something like a bacterial flagellum (function-wise, forget complexity and specificity, just give me "function" of a similar magnitude). No assumptions, no fairytales.

    3. Comment by computerist — January 12, 2010 @ 4:26 pm

  3. olegt Says:
    January 12th, 2010 at 4:42 pm

    My dear creationist hosts,

    Before you present your demands, I think you should first (1) define what you mean by information in the genome and (2) tell us how you would measure its amount in practice. From your ramblings I can tell that you don't mean information in the Shannon sense*, but what exactly you mean I have no idea. Don't point me to Dembski, he fails on point (2).

    All the best,

    O.

    *If you want to take the Shannon route, read this paper first: D. F. Styer, “Entropy and evolution,” Am. J. Phys. 76, 1031–1033 (2008). Here is a direct link: doi:10.1119/1.2973046.

    4. Comment by olegt — January 12, 2010 @ 4:42 pm

  4. Nick Matzke Says:
    January 12th, 2010 at 4:44 pm

    We're happy to answer these questions, but before a serious discussion can begin, we have to have a clear understanding of what you mean by "information." So: please define information. In particular, please tell us if new information has been generated in these two scenarios, and if so, where.

    1. A gene duplicates, producing 2 identical copies. Later, a mutation occurs which makes the new copy produce a protein that breaks down some environmental toxin. This selective advantage causes the altered copy to spread through the population. Initially this toxin-breakdown ability is weak and slow, but subsequent mutation events and selective sweeps fix a series of changes, say, 10, each improving the specificity and speed of the new reaction. End result: 2 genes, with (somewhat) different sequences, and (definitely) different functions, i.e. different functional sequences.

    2. A virus, say, chicken pox, invades a human. The adaptive immune system constantly generates billions of immune cells with different antigen receptors, each with different sequences in the variable receptor region. Of the billions & billions of immune cells, 1 has the ability to bind the invading virus proteins somewhat strongly. The cell carrying this antigen receptor proliferates, and through a process called affinity maturation, additional mutations to the receptor are made, and some of those produce stronger binding, and those cell lines proliferate, and within a few days a very strong receptor has been produced, resulting in permanent immunity against chicken pox. There is a function, highly-specific-binding-to-chicken-pox-virus, which didn't exist before in that human, that is caused by a specific functional DNA & amino acid sequence, which was not originally found in that human's genome (which is why they were suspectible to chicken pox).

    5. Comment by Nick Matzke — January 12, 2010 @ 4:44 pm

  5. Arthur Hunt Says:
    January 12th, 2010 at 5:39 pm

    Since we're trying to clarify things, would the process illustrated in Fig 7 of Thompson and Parker 2007 (provided near the end of this essay) constitute an increase in information?

    What about the polymerization of amino acids, without nucleic acids, in a way that gives rise to catalytic activities? Information gain, or no?

    6. Comment by Arthur Hunt — January 12, 2010 @ 5:39 pm

  6. computerist Says:
    January 12th, 2010 at 5:47 pm

    We're happy to answer these questions, but before a serious discussion can begin, we have to have a clear understanding of what you mean by "information."

    We're happy to answer these questions, but before a serious discussion can begin, we have to have a clear understanding of what you mean by "information."

    My dear resident chance and luck worshipers,

    You both got it backwards, I want to know what your information is, as far as I can tell the information baggage is not on my shoulders, but yours as all living systems are info-processing machines. If there is info "leaking in" as you say, please specify this environmental feedback, quantity it in a specific context/setting in which subsequently it would produce something of the functional magnitude of a bacterial flagellum.

    7. Comment by computerist — January 12, 2010 @ 5:47 pm

  7. olegt Says:
    January 12th, 2010 at 6:42 pm

    computerist,

    No reason to throw tantrums. We have not even begun to fight.

    If you have to know my take on quantifying information in biological systems, that would be Shannon's. Shannon's information is related to entropy and you can find implications of the second law of thermodynamics to evolution in the paper linked above.

    But from experience I know that for various reasons creationists don't like to use Shannon information and instead come up with new terms like specified complexity, functional information etc. As a rule, these terms are vague and they never tell you how that information can be measured by an objective observer. That's why both Nick and I are asking you to define what kind of information you are talking about. It does not matter what our definition of biological information is, it matters what yours is.

    So come on, big fella, tell us.

    8. Comment by olegt — January 12, 2010 @ 6:42 pm

  8. computerist Says:
    January 12th, 2010 at 7:25 pm

    That's why both Nick and I are asking you to define what kind of information you are talking about. It does not matter what our definition of biological information is, it matters what yours is.

    If you say information leaks from the environment, you presumably know what this information is. A sequence of 1111001111100000000000000001101111101011010111 binary digits, stored-in and transmitted from a medium may contain functional meaningful information to a receiver that can interpret it, but that information was plugged in by the an intelligent source, which supposedly knew what it was good for. What we are really talking about here is meta-information, information about other information, which is the information required to produce the effect in question. Shannon information is good for quantifying information, but in this case its quantifying meta-information, that comes externally before the transmit and receive cycle takes place.

    9. Comment by computerist — January 12, 2010 @ 7:25 pm

  9. Mung Says:
    January 12th, 2010 at 7:31 pm

    olegt:

    It does not matter what our definition of biological information is, it matters what yours is.

    Sigh.

    So when asked to defend their claims about information in the genome, what it is, how it gets there, what causes it to increase or decrease, the response is that what they mean by information does not matter.

    How stupid is that?

    10. Comment by Mung — January 12, 2010 @ 7:31 pm

  10. olegt Says:
    January 12th, 2010 at 7:35 pm

    computerist,

    So far you are the only one in this thread talking about information leaking from the environment. Neither Nick, not Arthur, nor myself said anything about it. And no, I still have no idea what your definition of information is. The term functional meaningful information does not ring the bell. Meta-information is equally vague. Please address the two points I posed above.

    11. Comment by olegt — January 12, 2010 @ 7:35 pm

  11. olegt Says:
    January 12th, 2010 at 7:36 pm

    Mung,

    I'm not saying that information does not matter, I'm trying to see what kind of information our friend computerist is talking about. So far he has failed to define it, so there is nothing to discuss. Maybe you can try.

    12. Comment by olegt — January 12, 2010 @ 7:36 pm

  12. IrynaB Says:
    January 12th, 2010 at 7:50 pm

    computerist,

    How do you like concept of Mutual Information?

    Suppose there are two environments, one white in winter, other brown in winter. Frequency of white environment is px. Suppose also there are two genes, one causing white fur in winter, other causing brown fur. Frequency of white gene is py. Joint distribution is pxy.

    Entropy of environment: Hx=px*log(px) + (1-px)*log(1-px)
    Entropy of gene: Hy=py*log(py)+(1-py)*log(1-py)
    Joint entropy: Hxy= sum pxy*log(pxy) [4 terms]

    Mutual information: Ixy = Hxy-Hx-Hy.

    If fur color has no selective value, then fur color and environment color are uncorrelated (Hxy=Hx+Hy) and Ixy=0. If white has selective advantage in white environment, and brown fur in brown environment, then gene frequencies will correlate with environment and Ixy>0 (Ixy=log(2) for perfect correlation).

    Back to you, computerist.

    13. Comment by IrynaB — January 12, 2010 @ 7:50 pm

  13. computerist Says:
    January 12th, 2010 at 7:51 pm

    So far you are the only one in this thread talking about information leaking from the environment. Neither Nick, not Arthur, nor myself said anything about it. And no, I still have no idea what your definition of information is. The term functional meaningful information does not ring the bell. Meta-information is equally vague. Please address the two points I posed above.

    I have repeatedly heard these claims. Do you deny these claims have been made by others from your "side"?

    If all you have is random mutations and natural selection, then you really have nothing, even if it did work, there is no way we could tell. It boils down to random errors through a blind filter plus a selection criteria carrying the only conditional Boolean did I survive. Nick M. seems to have already jumped on that bandwagon.

    14. Comment by computerist — January 12, 2010 @ 7:51 pm

  14. chunkdz Says:
    January 12th, 2010 at 8:11 pm

    Matzke wrote:

    1. A gene duplicates, producing 2 identical copies. Later, a mutation occurs which makes the new copy produce a protein that breaks down some environmental toxin. This selective advantage causes the altered copy to spread through the population. Initially this toxin-breakdown ability is weak and slow, but subsequent mutation events and selective sweeps fix a series of changes, say, 10, each improving the specificity and speed of the new reaction. End result: 2 genes, with (somewhat) different sequences, and (definitely) different functions, i.e. different functional sequences.

    For the sake of argument, let's call this an increase in information. Now remove the toxin from the environment.

    Has the information level just decreased since the gene no longer has a function?

    2. A virus, say, chicken pox, invades a human. The adaptive immune system constantly generates billions of immune cells with different antigen receptors, each with different sequences in the variable receptor region. Of the billions & billions of immune cells, 1 has the ability to bind the invading virus proteins somewhat strongly. The cell carrying this antigen receptor proliferates, and through a process called affinity maturation, additional mutations to the receptor are made, and some of those produce stronger binding, and those cell lines proliferate, and within a few days a very strong receptor has been produced, resulting in permanent immunity against chicken pox. There is a function, highly-specific-binding-to-chicken-pox-virus, which didn't exist before in that human, that is caused by a specific functional DNA & amino acid sequence, which was not originally found in that human's genome (which is why they were suspectible to chicken pox).

    Same thing. Now take chicken pox out of the environment. Have we just lost information because there is now no function? Is information therefore tied inextricably to function?

    I think before we define information, you need to rigorously define function for us.

    15. Comment by chunkdz — January 12, 2010 @ 8:11 pm

  15. computerist Says:
    January 12th, 2010 at 8:24 pm

    Suppose there are two environments, one white in winter, other brown in winter. Frequency of white environment is px. Suppose also there are two genes, one causing white fur in winter, other causing brown fur. Frequency of white gene is py. Joint distribution is pxy.

    If fur color has no selective value, then fur color and environment color are uncorrelated (Hxy=Hx+Hy) and Ixy=0. If white has selective advantage in white environment, and brown fur in brown environment, then gene frequencies will correlate with environment and Ixy>0 (Ixy=log(2) for perfect correlation).

    Supppose part of a binary sequence contained the hexadecimal equivalent 0×413839 which is 10000010011100000111001, this represented the color of a pixel on a monitor interpreted and rendered by a GPU to x.y location on the matrix. If this sub-sequence changed that would change the color, but it wouldn't change anything else, the new color would simply adapt to the monitor, hence illustrating the point of micro-evolution. There were additional sequences telling us where this color sequence starts and where it stops, a reserved constant bit-width of memory, thereby reading the sub-sequence will write some other color every time. The significant changes would come when we changed those start and stop characters. A bacterial flagellum, with its parts working simultaneously, is executing multiple mechanical "threads". These are examples which I require explaining. If a bio-molecular motor adapts its information in the same vein, then it shouldn't be hard to explain how this takes place.

    16. Comment by computerist — January 12, 2010 @ 8:24 pm

  16. IrynaB Says:
    January 12th, 2010 at 8:43 pm

    chunkdz

    Same thing. Now take chicken pox out of the environment. Have we just lost information because there is now no function? Is information therefore tied inextricably to function?

    Depends on level of analysis. In our species we all have broken vitamin C gene. That gives little information on within-species level (zero entropy). But if we look at vitamin C genes across species, then we see correlation with diet (positive entropy). Thus, broken vitamin C gene might inform us that we must eat vitamin C, but that our ancestors didn't have to.

    I think before we define information, you need to rigorously define function for us.

    Why not give it a try yourself, genius?

    17. Comment by IrynaB — January 12, 2010 @ 8:43 pm

  17. IrynaB Says:
    January 12th, 2010 at 8:51 pm

    computerist,

    Supppose part of a binary sequence contained the hexadecimal equivalent 0×413839 which is 10000010011100000111001, this represented the color of a pixel on a monitor interpreted and rendered by a GPU to x.y location on the matrix.

    Impressive that you know something about computers and hexadecimal notation. Now please give us your definition of information, or share your opinion about the definition of mutual information I gave.

    If this sub-sequence changed that would change the color, but it wouldn't change anything else, the new color would simply adapt to the monitor, hence illustrating the point of micro-evolution.

    That is strange usage of adapt. How does that compare to adaptive value of biological trait?

    18. Comment by IrynaB — January 12, 2010 @ 8:51 pm

  18. chunkdz Says:
    January 12th, 2010 at 9:00 pm

    IrynaB: "Depends on level of analysis. In our species we all have broken vitamin C gene. That gives little information on within-species level (zero entropy). But if we look at vitamin C genes across species, then we see correlation with diet (positive entropy). Thus, broken vitamin C gene might inform us that we must eat vitamin C, but that our ancestors didn't have to."

    Yeah, I like to watch National Geographic Channel too. Has little to do with my question though.

    Do you care to answer any of the very direct questions I asked?

    Why not give it a try yourself, genius?

    I guess that would be a no.

    19. Comment by chunkdz — January 12, 2010 @ 9:00 pm

  19. IrynaB Says:
    January 12th, 2010 at 9:05 pm

    Do you care to answer any of the very direct questions I asked?

    I did. Too bad for you the level is above your pay grade.

    20. Comment by IrynaB — January 12, 2010 @ 9:05 pm

  20. computerist Says:
    January 12th, 2010 at 9:13 pm

    If fur color has no selective value, then fur color and environment color are uncorrelated (Hxy=Hx+Hy) and Ixy=0. If white has selective advantage in white environment, and brown fur in brown environment, then gene frequencies will correlate with environment and Ixy>0 (Ixy=log(2) for perfect correlation).

    IrynaB, you seem to confuse (like all the other Darwinbots) the difference between correlation and causation. While mutual information is good for correlation, synchronizing the sub-sequences by turning some of the bits or genes on or off (as I have explained in my example) with the environment is nothing but a prime example of micro-evolution, they will inevitably "adapt" there is no question. Correlation between fur color and the environment may synchronize genes, but it doesn't cause the genes sub sequences to exist, in the right places. Try again.

    21. Comment by computerist — January 12, 2010 @ 9:13 pm

  21. computerist Says:
    January 12th, 2010 at 9:20 pm

    I will continue this discussion tomorrow…

    22. Comment by computerist — January 12, 2010 @ 9:20 pm

  22. IrynaB Says:
    January 12th, 2010 at 9:23 pm

    IrynaB, you seem to confuse (like all the other Darwinbots) the difference between correlation and causation.

    Perhaps you didn't realize that correlation does not imply causation but that they are highly correlated.

    Mutation causes existence of new genes. High frequency of new genes (and correlation with environment) is caused by selection.

    What is your definition of information?

    23. Comment by IrynaB — January 12, 2010 @ 9:23 pm

  23. computerist Says:
    January 12th, 2010 at 9:25 pm

    What is your definition of information?

    Whats yours? That is the real question.

    24. Comment by computerist — January 12, 2010 @ 9:25 pm

  24. nickmatzke Says:
    January 12th, 2010 at 9:35 pm

    Has the information level just decreased since the gene no longer has a function?

    [...]

    Same thing. Now take chicken pox out of the environment. Have we just lost information because there is now no function? Is information therefore tied inextricably to function?

    According to Meyer, the answer would apparently be YES. "Specified" = "function" in biology, according to Meyer. And Dembski, who Meyer cites. I.e. information = specified complexity = functional sequence.

    (One consequence of this view would be that a human resistant to chicken pox would LOSE a bunch of information when chicken pox is removed from the environment, and then, to be self-consistent, we would have to also say that the identical human would later GAIN that exact same bunch of information when the environment includes chicken pox again. This second event would falsify Meyer's attempted universal generalization that natural processes can never produce information. Q.E.D.)

    But from my own experience, I know that definitions of information proffered by evolutionists never satisfy creationists. So I just want to know what their definition is.

    I think before we define information, you need to rigorously define function for us.

    Biologists have a large literature discussing this. Usually they will say that function is whatever tends to give a selective advantage, and/or, if we are talking about an individual organism, whatever helps to satisfy some intention or instinct, i.e. a structure that helps eating or whatever.

    But it's not important what biologists would say, though, what's important is what IDists think. Or at least what Meyer would say.

    25. Comment by nickmatzke — January 12, 2010 @ 9:35 pm

  25. chunkdz Says:
    January 12th, 2010 at 10:23 pm

    Matzke: (One consequence of this view would be that a human resistant to chicken pox would LOSE a bunch of information when chicken pox is removed from the environment, and then, to be self-consistent, we would have to also say that the identical human would later GAIN that exact same bunch of information when the environment includes chicken pox again. This second event would falsify Meyer's attempted universal generalization that natural processes can never produce information. Q.E.D.).

    Ok. Let's carry this out to it's logical conclusion. If we take a human with genomic information = x and instantaneously place him on the surface of the moon, his genomic information has just decreased dramatically since few of his bodily functions serve to help him survive.

    If it seems ludicrous that the exact same genomic sequence can gain or lose information depending solely upon it's location, well, that is a matter of perspective. It does seem ludicrous to me. Kind of like saying that an Andrea Bocelli CD contains less information in it's case than it does when it is playing.

    I suspect Meyer wants to describe the intrinsic value of information in the genome, ie: that which is inherent in the sequence itself – while you are expressing your ideas in terms of the extrinsic value of the information in the genome, ie. dependent upon the environment.

    I haven't read the book so I am going to reserve judgement on this. It is quite likely that Meyer confuses the two perspectives, but the critics shouldn't take this as license to do the same.

    26. Comment by chunkdz — January 12, 2010 @ 10:23 pm

  26. Bradford Says:
    January 12th, 2010 at 10:56 pm

    computerist: I think before we define information, you need to rigorously define function for us.

    Nick Matzke: Biologists have a large literature discussing this. Usually they will say that function is whatever tends to give a selective advantage, and/or, if we are talking about an individual organism, whatever helps to satisfy some intention or instinct, i.e. a structure that helps eating or whatever.

    That's an interesting take Nick. We know that Meyer was principally focused on the origin of information. The origin of information and the origin of function are inextricably interconnected. Back to the chicken-egg dilemma. If function is whatever tends to give a selective advantage then we need criteria indicating what would be selected on planets where conditions are hospitable to life but where no life exists. What approach would you take Nick to discern what is selected prior to a point in time when a self-replicator can be observed much less defined with respect to its properties? Is it any wonder that OOL research has such a difficult time making a breakthrough? If function and selection are intertwined then a break in symmetry exists at an historic moment. What's a theorist to do?

    27. Comment by Bradford — January 12, 2010 @ 10:56 pm

  27. Bradford Says:
    January 12th, 2010 at 11:08 pm

    Olegt: computerist,

    So far you are the only one in this thread talking about information leaking from the environment.

    IrynaB: High frequency of new genes (and correlation with environment) is caused by selection.

    Is this an argument brewing between TT's first couple?

    28. Comment by Bradford — January 12, 2010 @ 11:08 pm

  28. nickmatzke Says:
    January 13th, 2010 at 2:36 am

    If it seems ludicrous that the exact same genomic sequence can gain or lose information depending solely upon it's location, well, that is a matter of perspective. It does seem ludicrous to me. Kind of like saying that an Andrea Bocelli CD contains less information in it's case than it does when it is playing.

    I suspect Meyer wants to describe the intrinsic value of information in the genome, ie: that which is inherent in the sequence itself – while you are expressing your ideas in terms of the extrinsic value of the information in the genome, ie. dependent upon the environment.

    I haven't read the book so I am going to reserve judgement on this. It is quite likely that Meyer confuses the two perspectives, but the critics shouldn't take this as license to do the same.

    I basically agree with all this, I was hopefully obviously basically doing a reductio ad absurdum of the "function defines information" argument.

    The problem, though, is that I'm not sure Meyer gives us anything much to go on in terms of a definition except for information = complex aperiodic sequence with a function.

    I suspect Meyer wants to describe the intrinsic value of information in the genome, ie: that which is inherent in the sequence itself – while you are expressing your ideas in terms of the extrinsic value of the information in the genome, ie. dependent upon the environment

    I suspect this is right, but AFAI can recall, there isn't anything in Signature in the Cell about "intrinsic value of information in the genome" and how we would be able to recognize it as distinct from e.g. randomly generated sequence. Let alone quantify it. Which is a pretty huge problem for supporters of Meyer's information –> intelligence argument.

    29. Comment by nickmatzke — January 13, 2010 @ 2:36 am

  29. nickmatzke Says:
    January 13th, 2010 at 3:52 am

    That's an interesting take Nick. We know that Meyer was principally focused on the origin of information. The origin of information and the origin of function are inextricably interconnected. Back to the chicken-egg dilemma. If function is whatever tends to give a selective advantage then we need criteria indicating what would be selected on planets where conditions are hospitable to life but where no life exists. What approach would you take Nick to discern what is selected prior to a point in time when a self-replicator can be observed much less defined with respect to its properties? Is it any wonder that OOL research has such a difficult time making a breakthrough? If function and selection are intertwined then a break in symmetry exists at an historic moment. What's a theorist to do?

    This, finally, is a worthwhile question. And it is the fundamental issue in Meyer's book. And I agree that pointing out Meyer's self-contradictions about the genome or pointing out that Meyer is wrong about stereochemistry and the genetic code do not strongly debunk this core argument. However, the existence of those problems should raise worries about the correctness of Meyer's core argument.

    Regarding Bradford's favorite, almost only, question, the origin-of-the-first-replicator question:

    There are a number of things that would have to be taken into account in a reasonable, thorough scientific consideration of the question of whether or not it is likely that the first replicator originated through a natural process, or through intelligent/divine intervention. In no particular order:

    1. Even if absolutely no natural explanation currently existed, that would not necessarily be good evidence for the proposition that no natural explanation is likely to exist. Making such an argument is just intrinsically difficult, given limited human knowledge.

    2. As it happens, a decent chunk of an explanation for the origin of the first replicators does exist, and appears to be growing bit-by-bit every year through progress in the origin-of-life field.

    3. In particular, progress in the OOL field is shown by the fact that several difficulties that used to be prominent, "unsolvable" chicken-and-egg puzzles, have in fact been solved. E.g. RNA world solved the DNA/protein chicken/egg puzzle. There is of course still some origin-of-the-RNA-world puzzle, but this is a smaller puzzle than the DNA/protein puzzle.

    4. The RNA World wasn't just a handy solution to a problem, it has turned out to be a highly successful research paradigm, with all kinds of spinoff research and practical benefits. This is just the sort of thing that encourages scientists to think they are on the right track.

    5. Origin-of-genetic-code studies have also been highly productive, there are thousands of articles on this and many research successes, thus getting from RNA World to RNA-protein world is on reasonably strong ground.

    6. The creationist method of argumentation in the OOL arena is similar to their argumentation in the fossil arena. I.e. (a) start with a gap, (b) find an intermediate, (c) creationist takes the new, smaller gaps and proclaims "I've discovered more gaps!" and also claims the new gaps are insoluble, just like the old one was supposed to have been. This whole approach is bankrupt, it is essentially a Xeno's paradox, where there is continual retreat, but science is never allowed to cross the finish line. (I like that. Copyright 2010 Nick Matzke.)

    7. Apart from the progress of OOL science, there are some positive reasons to think that the natural origin of replicators is likely.

    7a. When we trace the ancestors of modern extant life as far back as we can, we get to something much, much simpler than the modern biosphere. This didn't have to be true. A fuller argument on this point is here: http://pandasthumb.org/archive...

    7b. It just so happens that the fundamental biochemical basis of replication, i.e. semiconservative templating, ended up being fundamentally pretty simple. It turned out to be the kind of thing that just might maybe be within the reach of a chemical process. I think an argument can be made that e.g. it turned out to be simpler than Darwin thought it would be. This also didn't have to be the case.

    7c. The barrier between life and non-life doesn't appear to be absolutely distinct. In decreasing complexity, we have viruses, parasitic DNA elements, prions, and short, "naked" RNA parasites. From the other end, we have a variety of natural nonbiological phenomena that exhibit some lifelike qualities, if not all of them at once. This kind of thing weakens the claim that there is a fundamental metaphysical discontinuity in the life/nonlife distinction.

    7d. The barrier between replication and nonreplication is also not absolutely distinct. All replication is somewhat imperfect anyway, but there are various ways to have something between high-quality replication and just random assembly. Keywords are things like e.g. "statistical replicators", "compositional inheritance" (e.g. when a membrane vesicle splits, the daughters will inherit approximately the same percentage composition).

    8. Meyer's argument is basically that (a) natural processes haven't been observed to create new information, (b) intelligence has been observed to do this, (c) therefore intelligence. (a) is just wrong, it is disproven by e.g. the fact that gene duplication + mutation/selection for divergent function produces new functional sequence, i.e. new information on any reasonable definition. Therefore natural processes can create new information, therefore "information" is not some magical special thing requiring, basically, mystical intervention by Mind to produce, therefore Meyer's deductive argument fails.

    9. Even if we reduce Meyer's argument to (a) natural processes haven't been observed to create self-replicating chemical sequences, (b) intelligence has been observed to do this, (c) therefore intelligence must have created life, we have problems. (a) is called into serious question by points #1-7. Also, it is far from clear that (b) is even true at the moment, apart from trivial examples. Humans may find it trivial to "create information" of certain sorts, but it is definitely not trivial for humans to create chemical replicators. The sorts of stuff humans have produced that get closest either some from selection experiments, i.e. humans using evolutionary processes, or they come from basically "hacking" living systems.

    10. Another problem is that the evidence Meyer inputs into his argument more naturally supports the following: (a) natural processes can't produce information/replication, (b) humans can, (c) therefore humans caused life. There are no known examples of intelligence besides humans, what justification is there for extrapolating the existence of a general category called "intelligence", when we have but one example? The problem, of course, is that this argument is (a) more justifiable from Meyer's rules of inference (relying on observation and uniform experience), but (b) clearly wrong, since we have many positive reasons to think that humans have only recently come into existence.

    11. Meyer's rules of inference also lead to other problems. E.g., we could equally well argue, using Meyerian logic, that (a) natural processes haven't been observed to create structures taller than 1400 feet (the biggest observed natural structure is Paricutin volcano in Mexico, grew from 0 to 1,391 feet between 1942 and 1953), (b) intelligence has (Burj Khalifa tower in Dubai is 2720 feet tall), (c) therefore intelligence created all mountains higher than 1400 feet.

    There's more to say, but I'm going to bed!

    30. Comment by nickmatzke — January 13, 2010 @ 3:52 am

  30. nullasalus Says:
    January 13th, 2010 at 8:15 am

    Hello Nick,

    First, I'd like to compliment you on your posts here. Very calm, reasoned, and in general you don't make things personal. Thanks for that. Not sure we ever interacted before – possible, but I forget.

    Some questions/comments about your numbered points.

    1. Why do you contrast ID explanations with "natural" explanations? What makes an ID theory in this case.. what, supernatural? Unnatural? Non-natural? (Which of these words would you choose and why?)

    6. You aren't really suggesting every ID view is a 'creationist' one, are you? ID and teleological views aren't exclusively creationist, reliant on miracles, or 'gaps'. In fact, some suggest that the gaps can be filled precisely because of a teleological or design presence in nature. (In other words, it's not design v nature, because nature itself is not in opposition to design anyway.)

    7a and 7b fit just as well (and in some ways, more smoothly) with a teleological view than non-teleological. Or do you personally stay away from the whole teleology/non-teleology discussion, and focus more on people making gap or miracle claims?

    7c doesn't seem nearly to say what you think it does. That nonbiological phenomena never exhibit all the hallmarks of the 'lifelike', and that what phenomena they do exhibit is mostly analogous, seems to strengthen the idea that there is a fundamental distinction between life and non-life. I don't think you're suggesting hylozoism, are you?

    8. Given your tact in 7c, wouldn't the fact that "nature" can produce information end up as support for the claim that either nature was intelligent, or was a product of intelligence?

    9. Yes, humans can use evolutionary processes towards ends. Again, given your previous views about "weakening" distinctions, wouldn't this just weaken the case that an evolutionary or natural development was a development that took place absent a mind/intelligence? Also, I think calling the sort of information humans produce are 'trivial examples'. You really think an LHC is a trivial example? Or folding@home? Or, of course, all manner of genetic manipulation or bio-engineering on our part?

    9a. Are you making the claim that nature can create information, but *humans can't*?

    10. No known examples other than humans? What, computers don't count? Nature doesn't count? Other entities don't count? Maybe no known uncontested examples, but contesting is (as you probably know) easy.

    11. Again, there's this contrast of nature with intelligence, where "nature" does one thing and "intelligence" does another. But again, there are ID views (and more broadly, teleological views) that reject that contrast. And frankly, don't you think Meyer is going to admit that intelligence created all mountains, period, anyway?

    Also, if you're kind enough to respond, I have a side question I've been meaning to ask you for quite a while.

    * If I interpret you right, you take Intelligent Design to be unfalsifiable and non-scientific because of this. Would that mean you take science as unable to properly rule "X was" or "X was not designed/intended by a designer/God"?

    Thanks.

    31. Comment by nullasalus — January 13, 2010 @ 8:15 am

  31. nickmatzke Says:
    January 13th, 2010 at 12:23 pm

    Hi nullsalus — my argument is specifically responding to Meyer's argument, & Bradford's, not any conceivable argument, or any conceivable unusual construal of the terms as usually used in the ID argument.

    Meyer's argument focuses on "information", the claim that only nonmaterial "Mind"/"intelligence" can produce it (and Meyer does mean supernatural cause in the end), and the claim that it is very likely that natural processes cannot, primarily because (he claims) in all the cases where we know the causal story of where information came from, it came from intelligence, either directly from humans, or indirectly via e.g. a computer from humans. I.e., Meyer claims there is "universal human experience" in support of the idea that natural processes cannot create information/replication, and that only Mind can.

    There are obvious problems with this on all sorts of levels, I just tried to point those out. I do think this is basically all creationism in drag but that is a separate argument which will destroy the topic in this thread if we get on that.

    32. Comment by nickmatzke — January 13, 2010 @ 12:23 pm

  32. Bradford Says:
    January 13th, 2010 at 12:38 pm

    Nick:

    8. Meyer's argument is basically that (a) natural processes haven't been observed to create new information, (b) intelligence has been observed to do this, (c) therefore intelligence. (a) is just wrong, it is disproven by e.g. the fact that gene duplication + mutation/selection for divergent function produces new functional sequence, i.e. new information on any reasonable definition. Therefore natural processes can create new information, therefore "information" is not some magical special thing requiring, basically, mystical intervention by Mind to produce, therefore Meyer's deductive argument fails.

    A better rendition of what Meyer was saying is that when we observe digitally coded systems, correlated to function, beyond the cellular world, we are able to trace them back to an intelligent i.e. human source and this signifies that parallel systems found within cells should allow for consideration of an intelligent source (conscious intelligence). He did not say "We don't know how this works so it must have been God." To the contrary he is making the case that the nature of genetic information is uniquely suited to yield to intelligent sources in causal pathways. To those who would posit that chemical properties of matter mimick the appearance of symbolic meaning Meyer could argue, based on properties of nucleic acids and their expression mechanisms, that the symbolism is real. The implications of this for design are profound for the capacity to associate the physical with an abstraction is a fundamental properrty of conscious intelligence. There need be further indicators within nature able to distinguish between the differing perspectives and that merits a separate blog entry or better yet book follow-up.

    Gene duplication and subsequent mutations are a poor model on which to illustrate the capacity to generate information from ground zero. There is already a sophisticated messaging system in place which allows for begging of the underlying issue.

    33. Comment by Bradford — January 13, 2010 @ 12:38 pm

  33. Bradford Says:
    January 13th, 2010 at 12:51 pm

    Nick:

    2. As it happens, a decent chunk of an explanation for the origin of the first replicators does exist, and appears to be growing bit-by-bit every year through progress in the origin-of-life field.

    3. In particular, progress in the OOL field is shown by the fact that several difficulties that used to be prominent, "unsolvable" chicken-and-egg puzzles, have in fact been solved. E.g. RNA world solved the DNA/protein chicken/egg puzzle. There is of course still some origin-of-the-RNA-world puzzle, but this is a smaller puzzle than the DNA/protein puzzle.

    We witness growing knowledge of cellular functions and the spawning biotechnology trends that follow in their wake. I don't think it coincidental that the explosion of RNA interference industries and the growth in popularity of the RNA world largely coincided. Yet RNA does not answer the fundamental chicken-egg dilemma posed by Meyer which is not where did the enzymes come from but rather how does a process acquire a capacity for adaptation and evolution without information systems in place?

    34. Comment by Bradford — January 13, 2010 @ 12:51 pm

  34. chunkdz Says:
    January 13th, 2010 at 4:22 pm

    Matzke: I basically agree with all this, I was hopefully obviously basically doing a reductio ad absurdum of the "function defines information" argument.

    Does Signature in the Cell make a "function defines information" argument? The OP, at least, seems to be making an argument about interdependent systems within the cell (intrinsic), not function with regard to the environment (extrinsic).

    The problem, though, is that I'm not sure Meyer gives us anything much to go on in terms of a definition except for information = complex aperiodic sequence with a function.

    Does Signature in the Cell really define information as complex aperiodic sequence with a function?

    I suspect this is right, but AFAI can recall, there isn't anything in Signature in the Cell about "intrinsic value of information in the genome" and how we would be able to recognize it as distinct from e.g. randomly generated sequence. Let alone quantify it. Which is a pretty huge problem for supporters of Meyer's information –> intelligence argument.

    It is a difficult problem. An Andrea Bocelli CD in a world where the CD player hasn't been invented might be considered to be without function, without purpose, and therefore extremely low information content.

    And this would be utterly wrong.

    Sorry to keep asking about the book when I should just read it myself. I have the interest, just not the time.

    35. Comment by chunkdz — January 13, 2010 @ 4:22 pm

  35. nullasalus Says:
    January 13th, 2010 at 4:46 pm

    Nick,

    Fair enough. I don't think the terms I'm offering up are unusual construals by any means, but I understand if you want to really focus tight on a particular claim. I'll try to zero in on what pertains to that claim only.

    First, I'd really like to hear what distinction you have between "natural" and "supernatural". That seems central to what you're talking about here, and it'd help me better understand you. I think those terms are typically thrown around pretty carelessly, by ID proponents and critics both, so I like to try and get them nailed down.

    Second, Meyer makes the claim that minds (let's stick to talk of human minds right here) create information. Would you agree with that? It seems like a no-brainer (ha ha), but something you said in your list made me honestly wonder, so I'd like to clarify as much.

    Third, a fair chunk of Meyer's argument here seems to partly boil down to the claim that "minds" can do some things that "nature" can't. I'm not totally enthralled with the distinction either, but I'll roll with it. To start it off generally, in your own view, is there anything "mind" can do that "nature" can't? I could be wrong, but reading your replies here it sounds to me like you're saying 'Nature's generating information all the time. What intelligence does, nature can do.' Is that on target? If not, what are some distinctions?

    And again, thank you for the civility and insight here.

    36. Comment by nullasalus — January 13, 2010 @ 4:46 pm

  36. olegt Says:
    January 13th, 2010 at 5:17 pm

    nullasalus wrote:

    Second, Meyer makes the claim that minds (let's stick to talk of human minds right here) create information. Would you agree with that? It seems like a no-brainer (ha ha), but something you said in your list made me honestly wonder, so I'd like to clarify as much.

    This leads us back to the question raised above by Nick and myself. What do you, guys, mean by information? Before we can figure out whether human minds create information we need to determine how information is to be measured. Once that is agreed upon, we can measure the amount of information before and after and see whether the human mind increases the amount of information.

    If we are talking about Shannon information, which is basically entropy with a minus sign, then the answer is no. A human brain generates a lot of heat that gets dumped into the colder environment. This is an irreversible process that generates lots of entropy. How much? Let's estimate.

    For a grossly underestimated heat power of P = 1 W at the absolute temperature of T = 300 K, we are talking about an entropy flux of P/T = 0.0033 J/K per second. 1 bit of entropy is k log2 = 0.96 x 10^−23 J/K, so the entropy is created at a rate of 3.5 x 10^20 bits per second. That's 44 billion gigabytes per second! This amount of entropy (negative information) dwarfs the positive information the brain can reasonably produce.

    I'm sure our creationist friends will object that the mind produces high-quality functional, specified, super-duper information that nature simply can't, so it's not fair adding it to entropy. I'm sympathetic to that objection, but I would like to ask them—again!—how they would define and measure that special information that the mind produces.

    37. Comment by olegt — January 13, 2010 @ 5:17 pm

  37. chunkdz Says:
    January 13th, 2010 at 5:35 pm

    Olegt: This amount of entropy (negative information) dwarfs the positive information the brain can reasonably produce.

    Two questions:

    1) How do you know how much positive information a brain can reasonably produce?

    2) Why can't a brain/mind produce both positive and negative entropy discretely?

    38. Comment by chunkdz — January 13, 2010 @ 5:35 pm

  38. olegt Says:
    January 13th, 2010 at 6:03 pm

    chunkdz wrote:

    1) How do you know how much positive information a brain can reasonably produce?

    Estimates vary from 10^14 to 10^17 flops (floating-point operations per second). Since a flop generates 32 to 64 bits, we're talking about 10^16 to 10^19 bits per second. While that number is large, it's still only a small fraction of the negative information (entropy) generated by the living brain.

    2) Why can't a brain/mind produce both positive and negative entropy discretely?

    Not sure what you mean by that.

    39. Comment by olegt — January 13, 2010 @ 6:03 pm

  39. Bradford Says:
    January 13th, 2010 at 6:41 pm

    Olegt: This leads us back to the question raised above by Nick and myself. What do you, guys, mean by information?

    I'm told by some who would be in a position to know that there are ways of representing in binary language the information content of messaging systems but since that is not my field I'll stick with what I am familiar with namely, the sequencing of genomes and proteins. Information has multiple meanings as Meyer pointed out. In my comments when I raise a question about causal pathways I'm likely to cite sequential patterns as the subject of my inquiry. I'll discuss things like cellular transmitters and receivers and specific molecular mediums. The mirror question I have asked repeatedly is how randomly sequenced RNA in a prebiotic environment would react to yield an encoding system? This appears the more basic question as it obviously is antecedent to the example raised by Nick of gene duplication countering Meyer's position.

    40. Comment by Bradford — January 13, 2010 @ 6:41 pm

  40. chunkdz Says:
    January 13th, 2010 at 6:47 pm

    Not sure what you mean by that.

    If the brain stores positive information, and releases most of it's negative information to the atmosphere, can't we treat these as two discrete quantities?

    41. Comment by chunkdz — January 13, 2010 @ 6:47 pm

  41. Bradford Says:
    January 13th, 2010 at 6:51 pm

    Olegt:I'm sure our creationist friends will object that the mind produces high-quality functional, specified, super-duper information that nature simply can't, so it's not fair adding it to entropy.

    What point are you making with respect to the origin of DNA?

    42. Comment by Bradford — January 13, 2010 @ 6:51 pm

  42. nullasalus Says:
    January 13th, 2010 at 6:58 pm

    olegt,

    This leads us back to the question raised above by Nick and myself. What do you, guys, mean by information? Before we can figure out whether human minds create information we need to determine how information is to be measured. Once that is agreed upon, we can measure the amount of information before and after and see whether the human mind increases the amount of information.

    That's actually a better question for Nick than myself – I'm late into this conversation, and Nick's already been raising some interesting claims/criticisms re: humans and information, so it looks like there's already a definition in play here (see Nick's point 9.)

    And for the record, I'm not a big fan of some of the claims and distinctions I take Meyer to be making re: minds and "nature", or natural and "supernatural". That's why I'm chasing after some definitions of my own, such as 'natural and supernatural', and the distinction between minds and nature, etc.

    43. Comment by nullasalus — January 13, 2010 @ 6:58 pm

  43. ID guy Says:
    January 13th, 2010 at 7:21 pm

    olegt:
    From your ramblings I can tell that you don't mean information in the Shannon sense*, but what exactly you mean I have no idea.

    I am sure Meyer covered this in "Signature in the Cell".

    What Shannon wrote about really wasn't information, was it?

    It was mere complexity/ information carrying capacity.

    With biology information pertains to function.

    From "The origin of biological information and the higher taxonomic categories" (Meyer):

    Dembski (2002) has used the term “complex specified information” (CSI) as a synonym for “specified complexity” to help distinguish functional biological information from mere Shannon information–that is, specified complexity from mere complexity. This review will use this term as well.

    44. Comment by ID guy — January 13, 2010 @ 7:21 pm

  44. chunkdz Says:
    January 13th, 2010 at 7:28 pm

    ID Guy: With biology information pertains to function.

    Ludicrous.

    45. Comment by chunkdz — January 13, 2010 @ 7:28 pm

  45. Nick Matzke Says:
    January 13th, 2010 at 7:55 pm

    Hi nullasalus,

    Re: supernatural and natural. People get them confused when they try and define these from first principles. E.g. the philosopher Sober tries to argue that "numbers" are supernatural, according to the very odd definition of "supernatural" he comes up with.

    Where the terms make sense is history of western thought. Natural = things operating by the laws of physics that appear to be universally (or almost universally) operating now and in the past. This includes very complex products of the interaction of various laws, including stochastic/chance processes. Supernatural = miracles, basically, requiring the suspension of the aforementioned physical laws, typically by the action of God or a similar entity.

    You can pretty much boil down a supernatural event to violation of the First Law of Thermodynamics, which states that mass and energy can change form, but not be created or destroyed. All miracles I can think of violate this. Even if whole critters aren't poofing into existence, and if mass is conserved, e.g. God just rearranges some preexisting DNA base pairs to give them "information", then conservation of energy is still being violated, as it takes energy to rearrange those base pairs in that specific way.

    It is a difficult problem. An Andrea Bocelli CD in a world where the CD player hasn't been invented might be considered to be without function, without purpose, and therefore extremely low information content.

    And this would be utterly wrong.

    I kind of agree, but look at it in two other ways.

    (1) from the perspective of biology, this might be the way things actually are. E.g., if a gene loses function (e.g., primates didn't need the gene to synthesize Vitamin C, since they got it from their fruity diet), then it decays through mutation and neutral drift in *exactly the same way* that random, nonfunctional sequence does.

    (2) Imagine if you were a primitive illiterate tribesman with no concept of complex technology, codes, etc. and came across the CD. Would it have any "information" from your perspective? Would you think it was obviously "designed"? Or would you use it as a plate?

    (3) Imagine you are modern scientist, but you come across a piece of alien technology, but so advanced and so remote from your experience, that you are in about the same relative position as a tribesman looking at a CD. Would you even conclude that the item was a piece of technology? Would you successfully perceive the "information"?

    Tough questions. I suspect that all "information" in the creationist "meaning" sense is context-dependent, i.e. meaningful in one context and not others. But this means that in biology, "information" is whatever sequences function, and if this is so, then Meyer is screwed, because natural processes can clearly produce this sort of information, so his negative generalization about natural processes is sunk.

    46. Comment by Nick Matzke — January 13, 2010 @ 7:55 pm

  46. Nick Matzke Says:
    January 13th, 2010 at 8:00 pm

    Just so we get everyone crystal clear that Meyer really does argue that "information" = complex sequence that is function:

    Thus, molecular biologists beginning with Francis Crick have equated biological information not only with improbability (or complexity), but also with "specificity," where "specificity," or "specified", has meant "necessary to function."

    Thus, in addition to a quantifiable amount of Shannon information (or complexity), DNA also conrains information in the sense of Webster's second definition: it contains "alternative sequences or arrangements of something that produce a specific effect." Although DNA does not convey information that is received, understood, or used by a conscious mind, it does have information that is received and used by the cell's machinery to build the structures critical to the mainrenance of life. DNA displays a property — functional specificity — that transcends the merely mathematical formalism of Shannon's theory.

    [p. 110]

    Is this significant? In fact, it is profoundly mysterious. Apart from the molecules comprising the gene-expression system and machinery of the cell, sequences or structures exhibiting such specified complexity or specified information are not found anywhere in the natural — that is, the nonhuman — world. Sequences and structures exhibiting either redundant order or mere complexity are common in the chemical substrate of nature. But structures exhibiting specified complexity are completely unknown there apart from DNA, RNA, and proteins. As the origin-of-life biochemist Leslie Orgel observes: "Living organisms are distinguished by their specified complexity. Crystals . . . fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity." Nevertheless, human artifacts and technology — paintings, signs, written text, spoken language, ancient hieroglyphics, integrated circuits, machine codes, computer hardware and software — exhibit specified complexity; among those, software and its encoded sequences of digital characters function in a way that most closely parallels the base sequences in DNA.

    Thus, oddly, at nearly the same time that computer scientists were beginning to develop machine languages, molecular biologists were discovering that living cells had been using something akin to machine code or software all along. To quote the information scientist Hubert Yockey again, "The genetic code is constructed to confront and solve the problems of communication and recording by same principles found … in modern communication and computer codes." Like software, the coding regions of DNA direct operations within a complex material system via highly variable and improbable, yet also precisely specified, sequences of chemical characters. How did these digitally encoded and specifically sequenced instructions in DNA arise? And how did they arise within a channel for transmitting information? (pp. 109-110, italics original)

    As noted, biological information, such as we find in DNA and proteins, comprises two features: complexity and functional specificity. Computer codes and linguistic texts also manifest this pair of properties ("complexity" and "specificity"), what I have referred to throughout this book as specified information. Although a computer program may be similar to DNA in many respects and dissimilar in others, it exhibits a precise identity to DNA insofar as both contain specified complexity or specified information. (p. 386, italics original)

    Of course, insofar as the term "information" connotes semantic meaning, it does function as a metaphor within biology. That does not mean, however, that the term functions only metaphorically or that origin-of-life biologists have nothing to explain. Though information theory has a limited application in describing biological sysrems, it has succeeded in rendering quantitative assessments of the complexity of biomacromolecules. Further, experimental work has established the functional specificity of the base sequences in DNA and amino acids in proteins. Thus, the term "information" as used in biology refers to two real and contingent properties: complexity and functional specificity. (p. 387, italics original)

    The origin of specified complexity, to which the term "information" in biology commonly refers, therefore does require explanation, even if the concept of information connotes only complexity in Shannon information theory and even if it connotes meaning in common parlance, and even if it has no explanatory or predictive value in itself. Instead, as a descriptive (rather than an explanatory or predictive) concept, the term "information" (understood as specified complexity) helps to define an essential feature of life that origin-of-life researchers must explain "the origin of." So, only where information connotes subjective meaning does it function as a metaphor in biology. Where it refers to complex functional specificity, it defines a feature of living systems that calls for explanation every bit as much as, say, a mysterious set of inscriptions on the inside of a cave. (p. 388, emphasis original)

    47. Comment by Nick Matzke — January 13, 2010 @ 8:00 pm

  47. Nick Matzke Says:
    January 13th, 2010 at 8:15 pm

    Meant to say:

    Just so we get everyone crystal clear that Meyer really does argue that "information" = complex sequence that is functional:

    48. Comment by Nick Matzke — January 13, 2010 @ 8:15 pm

  48. chunkdz Says:
    January 13th, 2010 at 10:20 pm

    Matzke: Just so we get everyone crystal clear that Meyer really does argue that "information" = complex sequence that is functional

    Thanks for the quotes Nick. I was truly prepared to throw Meyer under the bus if he was arguing using extrinsic function as part of information. The quotes, however, show that he is talking about intrinsic function of DNA. I don't have a problem with that.

    I kind of agree, but look at it in two other ways.

    (1) from the perspective of biology, this might be the way things actually are. E.g., if a gene loses function (e.g., primates didn't need the gene to synthesize Vitamin C, since they got it from their fruity diet), then it decays through mutation and neutral drift in *exactly the same way* that random, nonfunctional sequence does.

    No problem with that.

    (2) Imagine if you were a primitive illiterate tribesman with no concept of complex technology, codes, etc. and came across the CD. Would it have any "information" from your perspective? Would you think it was obviously "designed"? Or would you use it as a plate?

    (3) Imagine you are modern scientist, but you come across a piece of alien technology, but so advanced and so remote from your experience, that you are in about the same relative position as a tribesman looking at a CD. Would you even conclude that the item was a piece of technology? Would you successfully perceive the "information"?

    Now you're touching on what fuels my suspicion about design. Not only are we beginning to be able to perceive the information at this time in history, but DNA looks like the future of our own software designs. Remarkable since it hasn't been markedly imroved upon in nearly 4 billion years.

    Also, about the time Feynman was suggesting we look toward the nanoscale for our own designs we began discovering that the cell had already been manufacturing highly advanced nanotechnology – for nearly 4 billion years.

    As Mike Gene said, "Looking into a living cell is like looking at the future of our own designs".

    We are no longer the proverbial cavemen wondering what the CD could possibly be. Our own technological enlightenment has illuminated the fact that we ourselves are highly advanced technology.

    And we have been for nearly 4 billion years.

    49. Comment by chunkdz — January 13, 2010 @ 10:20 pm

  49. nullasalus Says:
    January 13th, 2010 at 10:20 pm

    Nick,

    Re: supernatural and natural. People get them confused when they try and define these from first principles. E.g. the philosopher Sober tries to argue that "numbers" are supernatural, according to the very odd definition of "supernatural" he comes up with.

    See, one problem popping up right away here is…

    Where the terms make sense is history of western thought. Natural = things operating by the laws of physics that appear to be universally (or almost universally) operating now and in the past. This includes very complex products of the interaction of various laws, including stochastic/chance processes. Supernatural = miracles, basically, requiring the suspension of the aforementioned physical laws, typically by the action of God or a similar entity.

    ..Given your own definition, of course "numbers" are supernatural if you're a platonist on (or arguably, any kind of realist regarding) math. Abstracts don't "operate by the laws of physics", so if one's a realist about them, what else can they be? Further, what about things like intentionality – are you saying that such a thing is fundamentally part of physics somehow? Or is unreal? Or is it going to end up supernatural too?

    But more than that, "history of western thought" doesn't help out much here either, because that's going to span everyone from Aristotle to Scotus to Kant to Hume, etc. And that's going to mean vastly different views on what natural is, what supernatural is, and even what miracle is. Sure, the terms probably make sense within those different contexts, but we've got to pick a context. Not to mention that western thought largely stuck to defining miracles in relation to "first principles" anyway, in whatever variety of ways.

    And the context you seem to be picking here has other problems.

    You can pretty much boil down a supernatural event to violation of the First Law of Thermodynamics, which states that mass and energy can change form, but not be created or destroyed. All miracles I can think of violate this. Even if whole critters aren't poofing into existence, and if mass is conserved, e.g. God just rearranges some preexisting DNA base pairs to give them "information", then conservation of energy is still being violated, as it takes energy to rearrange those base pairs in that specific way.

    But we don't need miracles to "rearrange some pre-existing DNA base pairs to give them "information"", unless you're going to insist this is something humans don't do or can't do even in principle. God wouldn't necessarily have to specifically "rearrange" anything – He could simply have set up nature to produce this result one way or the other. Unless Meyer is ruling this out, there you have something occurring in nature, no miracle needed, and still it's going to be best explained by design.

    But let's say Meyer specifically insists that what took place is an intervening act – some effect X (say the origin of life) would never have taken place without an intervening hand, the effect took place, so clearly there was an intervention. That's great, but it doesn't get you to a miracle on its own. It doesn't even get you to a violation of the 1st law of thermodynamics. It can simply be that our conception of what comprises our universe is just incorrect or incomplete.

    To give an example, let's say I'm running a computer simulation of chemical interactions, trying to come up with life originating. I get bored since the system is getting nowhere, hit the admin panel, and a few clicks later – *poof*. Life is now in the program. If someone's watching this (either an AI in the simulation, or just someone watching from another terminal) and goes "Ah! Look at that! Intervention! Miracle! First law of thermodynamics, violated!" they'd be wrong. The First Law is chugging along just fine – the system is just bigger than and/or different from what they thought.

    I'm going through all of this because you claim that Meyer is saying 'nature can't do this on its own, but mind/intelligence can' and Meyer means supernatural by that. I'd like to know where Meyer makes the mind/intelligence = supernatural link, but I don't think it's unreasonable he may have done that. But I'd also suspect Meyer would argue ID can be strongly inferred without having to appeal to violations of the first law of thermodynamics, and that countering Meyer's claim that "mind/intelligence" is needed for or is the best explanation for given events in or features in biology is going to have to grapple with some pretty annoying (let's be frank) topics.

    Specifically, it seems like a Meyer critic going to need at the very least A) An account of nature that renders it void of mind/intelligence [Otherwise the only response to Meyer is agnosticism or ultimately agreement, however qualified] and B1) An account of mind/intelligence that doesn't render humanity or any intelligent agent 'supernatural' by definition (If "nature" is devoid of these things, but humans at the least have them…) or B2) A claim that mind/intelligence does not really exist, full stop (Its own bag of worms.)

    50. Comment by nullasalus — January 13, 2010 @ 10:20 pm

  50. olegt Says:
    January 13th, 2010 at 11:11 pm

    chunkdz wrote:

    If the brain stores positive information, and releases most of it's negative information to the atmosphere, can't we treat these as two discrete quantities?

    To see why this does not work, let's translate this to a more familiar setting of personal banking.

    Suppose you borrow money from a friend on a regular basis. You store the cash (the equivalent of positive information) in your wallet and give him promissory notes (megative information). Although the amount of cash in your wallet is growing you cannot claim that you are making money: you are simply transferring it from your friend into your wallet.

    In the example I worked out, the brain is reducing overall disorder in the Universe by doing calculations, but at the same time it is increasing the same disorder by adding entropy as a result of irreversible thermal processes. The estimate shows that the overall amount of disorder tends to increase because the computational output of the brain is quite a bit smaller than the entropy it produces. This is in agreement with the work of information theorists like Charles Bennett. See C. H. Bennett, "Notes on Landauer's principle, Reversible Computation and Maxwell's Demon," arXiv:physics/0210005.

    51. Comment by olegt — January 13, 2010 @ 11:11 pm

  51. nickmatzke Says:
    January 14th, 2010 at 2:51 am

    I was truly prepared to throw Meyer under the bus if he was arguing using extrinsic function as part of information. The quotes, however, show that he is talking about intrinsic function of DNA.

    What do you mean by this distinction? It's not in Meyer's book.

    Re: natural/supernatural and miracles —

    Do numbers violate the conservation of mass and energy? Nope. Ergo, not a miracle, not supernatural.

    Do humans? Nope. Not a miracle, not supernatural.

    Does God poofing animals into existence violate it? Yep.

    Does God poofing DNA from one arrangement into another violate it? Yep.

    These last two things are basically the statement "it happened by wholly mysterious means equivalent to magic." It's fine if you think that, I just don't see any point, except legal/political, in trying to hide the fact that a miracle is being invoked, by pretending that those sorts of events are the same thing as human action or numbers. If one is arguing for miracles, be proud and own it.

    God wouldn't necessarily have to specifically "rearrange" anything – He could simply have set up nature

    This would mean natural processes could and did create functional specified sequence. Which is precisely what Meyer spends the book arguing against.

    He could simply have set up nature to produce this result one way or the other.

    I think this version of the front-loading idea is one of silliest things the ID movement has come up with. The information in the DNA sequence which produces the bacterial flagellum (or whatever) is inherent in the setup of the Big Bang? What does that even mean? Where is the "information" when the Universe is 200,000 years old and essentially a huge hot ball of superheated hydrogen? Oh, and the one known natural process that might actually have a shot at letting a superintelligent universe creator set up the universe to produce functional sequences, namely natural selection, is specific ruled to be incapable of this role by the ID movement.

    Frontloading-the-universe is basically an incoherent copout that is popular only because it gives some fig leaf of a cover to the notion that ID isn't necessarily talking about miracles.

    He could simply have set up nature to produce this result one way or the other. Unless Meyer is ruling this out,

    Meyer is ruling this out. Meyer says natural laws, i.e. the setup of nature, cannot produce information. This is the whole point of his book.

    there you have something occurring in nature, no miracle needed, and still it's going to be best explained by design.

    I guess you are trying to defend Behe's frontloading proposal in Edge of Evolution, but (a) it's silly for the reason I mentioned above, and (b) we're supposed to be talking about Meyer's book, which is hard when you haven't read it and keep dragging the discussion off in other directions.

    52. Comment by nickmatzke — January 14, 2010 @ 2:51 am

  52. nullasalus Says:
    January 14th, 2010 at 4:25 am

    Nick,

    This would mean natural processes could and did create functional specified sequence. Which is precisely what Meyer spends the book arguing against.

    If you're telling me that Meyer's argument is "natural processes cannot and did not create functional specified sequence, *and even an intervention or setup by an intelligent agent cannot change this*", well hell. I'd ask for proof, but frankly, if that's really your claim I'm going to have to finish the book and see where this comes up. Because that would be saying that nature is so hobbled, not even actual full-blown ID can do anything with it in principle.

    Bradford, Chunk, anyone else – can you second this claim? Is Meyer really saying this?

    I think this version of the front-loading idea is one of silliest things the ID movement has come up with. The information in the DNA sequence which produces the bacterial flagellum (or whatever) is inherent in the setup of the Big Bang? What does that even mean? Where is the "information" when the Universe is 200,000 years old and essentially a huge hot ball of superheated hydrogen?

    Where are the contents of the Library of Congress on a thin piece of ink-stained plastic? How can a 100k program procedurally generate megs upon megs of content?

    Oh, and the one known natural process that might actually have a shot at letting a superintelligent universe creator set up the universe to produce functional sequences, namely natural selection, is specific ruled to be incapable of this role by the ID movement.

    I'd like you to support what you're claiming here. You're saying the "ID movement" – presumably, everyone at the Discovery Institute included – thinks that a designer is incapable, even in principle, of using evolution to create. Or that if evolution is involved, it cannot be ID. I have some deep disagreements with the "ID Movement". But I've read enough of their proponents' writing, and even corresponded with them, to know that this claim – that "natural selection", even if guided by and/or utilized by a designer, is incapable of accomplishing much of anything – is bunk. Utter, complete bunk.

    Frontloading-the-universe is basically an incoherent copout that is popular only because it gives some fig leaf of a cover to the notion that ID isn't necessarily talking about miracles.

    The idea is entirely coherent – I don't know why you think otherwise. I stand by the points I made about "miracles" and the first law of thermodynamics as well. Maybe you're saying that okay, maybe they don't have to be talking about miracles, but you know what they *really* mean. Stand by that if you want, but that's just uninteresting to me. I avoid the psychoanalyzing games.

    I guess you are trying to defend Behe's frontloading proposal in Edge of Evolution, but (a) it's silly for the reason I mentioned above, and (b) we're supposed to be talking about Meyer's book, which is hard when you haven't read it and keep dragging the discussion off in other directions.

    No, and I didn't say word one about Behe. In fact, I happily dropped all talk of other ID proponents when you requested – you're the one who brought them up again. I asked you about how you're defining natural v supernatural, I pointed out problems with how you're defining these things as well as the talk about the apparent unavoidability of miracles. I happily dropped quite a lot of other questions and comments I had for the sake of zeroing in on what's relevant to Meyer's claims, and your criticisms of Meyer. I pointed out that either if nature is set up to unfold a certain way, or if an actual intervention takes place, we're not suddenly at "violations of natural law" or "miracles" or otherwise.

    What's more – come on, Nick, be fair here. You're taking shots at the "ID Movement" as a whole when I'm not bringing them up, then when I point out a problem with one of your claims you suddenly guess I had Behe in mind, then chastize me or bringing up Behe when we're talking about Meyer. That's like "Don't think pink", except you're rapping me just because you thought I thought about pink.

    53. Comment by nullasalus — January 14, 2010 @ 4:25 am

  53. Bradford Says:
    January 14th, 2010 at 7:34 am

    Nick: These last two things are basically the statement "it happened by wholly mysterious means equivalent to magic." It's fine if you think that, I just don't see any point, except legal/political, in trying to hide the fact that a miracle is being invoked, by pretending that those sorts of events are the same thing as human action or numbers. If one is arguing for miracles, be proud and own it.

    This is a specious argument. There is simply no way to make an historic determination about contraventions of natural laws or whether an intelligent source had to contravene natural laws to effect a biological result. Humans can alter the genetics of organisms. This was indirectly possible even prior to advanced technology. It was accomplished through breeding practices. If a billion years from now humans are extinct but microorganisms and mammals altered by humans persist, there would be no certain way of determining the intelligent input into the genomes of altered organisms for extraterrestrial visitors.

    54. Comment by Bradford — January 14, 2010 @ 7:34 am

  54. Bradford Says:
    January 14th, 2010 at 8:36 am

    Nick:

    Frontloading-the-universe is basically an incoherent copout that is popular only because it gives some fig leaf of a cover to the notion that ID isn't necessarily talking about miracles.

    Front loading the universe generally refers to laws of nature which enable life in this universe. Constant values, anthropic principles- that sort of thing.

    55. Comment by Bradford — January 14, 2010 @ 8:36 am

  55. nickmatzke Says:
    January 14th, 2010 at 12:31 pm

    But I've read enough of their proponents' writing, and even corresponded with them, to know that this claim – that "natural selection", even if guided by and/or utilized by a designer, is incapable of accomplishing much of anything – is bunk. Utter, complete bunk.

    Sure it's bunk, but I never said that ID people said that NS was incapable with intelligent help. Why would I say that? They all argue that NS, without that designer intervention, can't accomplish anything very important, like building flagella. Everyone from YECs to Behe argues that — they argue that natural processes, especially the mutation/selection mechanism, are incapable of producing complex functional biological structures, like flagella, new information, etc.

    It's what Meyer says also. Again and again and again. Why are you denying that this is what they say?

    Of course they think that with intelligent intervention, NS can do stuff, but the key factor there is the intervention, that's the whole freakin' point of them criticizing NS!

    But anyway, we've been around this merry-go-round a few times in this thread already, I'm not really interested in arguing with people who take the obvious main points made by the ID leaders like Meyer, and then claim that they aren't saying those things at all.

    So unless the topic returns to Meyer and his information argument, I'm done. See ya!

    56. Comment by nickmatzke — January 14, 2010 @ 12:31 pm

  56. chunkdz Says:
    January 14th, 2010 at 2:01 pm

    Olegt wrote:

    In the example I worked out, the brain is reducing overall disorder in the Universe by doing calculations, but at the same time it is increasing the same disorder by adding entropy as a result of irreversible thermal processes. The estimate shows that the overall amount of disorder tends to increase because the computational output of the brain is quite a bit smaller than the entropy it produces. This is in agreement with the work of information theorists like Charles Bennett. See C. H. Bennett, "Notes on Landauer's principle, Reversible Computation and Maxwell's Demon," arXiv:physics/0210005.

    We can measure the amount of information before and after and see whether the human mind increases the amount of information.

    If we are talking about Shannon information, which is basically entropy with a minus sign, then the answer is no.

    So, Mozart didn't actually create any information – because his brain gave off too much heat??

    57. Comment by chunkdz — January 14, 2010 @ 2:01 pm

  57. ID guy Says:
    January 15th, 2010 at 10:09 am

    Nick Matzke:
    Natural = things operating by the laws of physics that appear to be universally (or almost universally) operating now and in the past.

    Except that those laws of physics are part of the evidence for Intelligent Design.

    Everyone from YECs to Behe argues that — they argue that natural processes, especially the mutation/selection mechanism, are incapable of producing complex functional biological structures, like flagella, new information, etc.

    That is false.

    It isn't "natural" processes per se- it is blind and undirected processes.

    58. Comment by ID guy — January 15, 2010 @ 10:09 am

  58. ID guy Says:
    January 15th, 2010 at 10:14 am

    Information- as it pertains to this debate- is the difference between Stonehenge and stones.

    It is the difference between artifacts and rocks/ clay

    It is the difference between arson and a fire.

    It is the difference between a murder and "natural" death.

    It is the difference between meaning and gibberish.

    59. Comment by ID guy — January 15, 2010 @ 10:14 am

  59. ID guy Says:
    January 15th, 2010 at 3:42 pm

    chunkdz:
    So, Mozart didn't actually create any information – because his brain gave off too much heat??

    It saves on the heating bill. :cool:

    60. Comment by ID guy — January 15, 2010 @ 3:42 pm

  60. ID guy Says:
    January 15th, 2010 at 3:48 pm

    Best Look Ever at Life’s Smallest Rotary Motor- a close look at F-ATP & ATP synthase. :cool:

    61. Comment by ID guy — January 15, 2010 @ 3:48 pm

  61. nickmatzke Says:
    January 15th, 2010 at 5:19 pm

    ID guy Says:
    January 15th, 2010 at 10:14 am

    Information- as it pertains to this debate- is the difference between Stonehenge and stones.

    It is the difference between artifacts and rocks/ clay

    It is the difference between arson and a fire.

    It is the difference between a murder and "natural" death.

    It is the difference between meaning and gibberish.

    That's fine, but Meyer says it is quantifiable and that natural processes cannot create it, so please tell us how to quantify information so that we may test his key claim.

    62. Comment by nickmatzke — January 15, 2010 @ 5:19 pm

  62. Mung Says:
    January 15th, 2010 at 9:31 pm

    olegt:

    I'm not saying that information does not matter, I'm trying to see what kind of information our friend computerist is talking about. So far he has failed to define it, so there is nothing to discuss. Maybe you can try.

    It's really quite simple. Mutations are random with respect to fitness. In order to have a genome full of anything other than random gunk it's necessary to test against the environment (you know, that whole natural selection replaces teleology thing). This is how "information" get into the genome. This is the Darwinian story.

    You've seriously never heard of this explanation for information in the genome? I knew right away what computerist was talking about.

    63. Comment by Mung — January 15, 2010 @ 9:31 pm

  63. ID guy Says:
    January 15th, 2010 at 11:05 pm

    nickmatzke:
    That's fine, but Meyer says it is quantifiable and that natural processes cannot create it, so please tell us how to quantify information so that we may test his key claim.

    Blind, non-goal oriented processes- and it has to do with origins.

    I said:

    Information- as it pertains to this debate- is the difference between Stonehenge and stones.

    Reduction- what can each be reduced to?

    Stones can be reduced to blind and non-goal oriented processes whereas Stonehenge cannot.

    So we (try to) determine what else is needed, then figure out a way to measure it.

    There you have it.

    To test Meyer's claim all you have to do is show that blind and non-goal oriented processes can produce a living organism from inanimate matter.

    IOW it really doesn't matter what Meyer says or what Dembski says or what Behe says or what I say.

    YOU have the power.

    YOU can show us that a designer is not needed just by substantiating your claims.

    Imagine that…

    64. Comment by ID guy — January 15, 2010 @ 11:05 pm

  64. computerist Says:
    January 16th, 2010 at 2:28 am

    Olegt wrote:

    For a grossly underestimated heat power of P = 1 W at the absolute temperature of T = 300 K, we are talking about an entropy flux of P/T = 0.0033 J/K per second. 1 bit of entropy is k log2 = 0.96 x 10^−23 J/K, so the entropy is created at a rate of 3.5 x 10^20 bits per second. That's 44 billion gigabytes per second! This amount of entropy (negative information) dwarfs the positive information the brain can reasonably produce.

    I hope you know that this calculation – which I applaud you for – does not help the Darwinian case in anyway. If the brain can only produce an insignificant degree of qualitative – positive information out of the 44 billion gb's/second throughput then how much more of that qualitative meta-information would you expect "leaking from the environment" in comparison.

    65. Comment by computerist — January 16, 2010 @ 2:28 am

  65. computerist Says:
    January 16th, 2010 at 3:37 am

    I'm sure our creationist friends will object that the mind
    produces high-quality functional, specified, super-duper information that nature simply can't, so it's not fair adding it to entropy. I'm sympathetic to that objection, but I would like to ask them—again!—how they would define and measure that special information that the mind produces.

    Olegt, automotive engineers have designed 10 plans for car engine designs, lots of "super-duper" information in there. It turns out 2 / 10 of these work, 1 / 2 of these working designs produces more hp, but takes up more fuel. Regardless of the displacement per one complete engine cycle, the 2 working designs – a composition extracted from meta-information – with the help of an assembly line produced the desired physical effect. Now the probability of this positive information achieving the effect, with respect to your calculation decreases since while alot of meta-information in the 8 out of 10 designs was considered qualitative, they were not able to be taken into its objective physical state. This fraction of a fraction is considered to be the real positive information that is necessary to explain something like a molecular mechine of the functional magnitude of a bacterial flagellum. Its "super-duper" as you say.

    66. Comment by computerist — January 16, 2010 @ 3:37 am

  66. ID guy Says:
    January 16th, 2010 at 10:36 am

    To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    67. Comment by ID guy — January 16, 2010 @ 10:36 am

  67. computerist Says:
    January 16th, 2010 at 9:42 pm

    To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    Hi ID guy, I'm not sure if this is a response to me, if it is then it doesn't apply.

    68. Comment by computerist — January 16, 2010 @ 9:42 pm

  68. Bradford Says:
    January 16th, 2010 at 11:14 pm

    Any information measure defined in terms of probabilities is potentially useful in all areas where the probability theory is applied: in most sciences and in many of the humanities. And, information appears in different spheres, such as biology, "Life, too, is digital information written in DNA" {Ridley, 2000, p.16}, and in physics, "Giving us its as bits, the quantum presents us with physics as information" {Wheeler, 1990, p.7}. Or, a bit differently, to work out "physics from Fisher information" {Frieden, 1998}.

    here

    69. Comment by Bradford — January 16, 2010 @ 11:14 pm

  69. nullasalus Says:
    January 17th, 2010 at 2:43 am

    Nick,

    Sure it's bunk, but I never said that ID people said that NS was incapable with intelligent help. Why would I say that? They all argue that NS, without that designer intervention, can't accomplish anything very important, like building flagella.

    Nick, you did say otherwise. From earlier:

    Oh, and the one known natural process that might actually have a shot at letting a superintelligent universe creator set up the universe to produce functional sequences, namely natural selection, is specific ruled to be incapable of this role by the ID movement.

    I've been insisting from the start here that "natural" forces are, by ID views, entirely capable of accomplishing creative acts of the kind Meyer credits mind and intelligence. You've been responding that, no no no, for ID nature is incapable of these things, off the table, it must be a miracle, it must be supernatural! Now you're admitting that, sure, nature could be capable of these things by ID views – it would just point at something other than unguided, blind nature. It requires no miracle (and what qualifies as a "miracle" is a debated thing anyway), it requires no violation of the first law of thermodynamics, etc.

    So no, "nature" is not ruled to be incapable of these things by the "ID movement". Nature as conceived by some – "blind, unguided" natural forces – are inferred as incapable. Or more specifically, "nature" is capable of certain things, but the fact that it's capable of them is good reason to infer that they're anything but blind or unguided. In fact, we should infer there's intelligence and agency at work.

    It's what Meyer says also. Again and again and again. Why are you denying that this is what they say?

    Because your criticisms and interpretations of "what they say" are, in my view, falling drastically flat. And I don't even think ID is science. Granted, I'm sympathetic socially and philosophically, but if Meyer really was making the argument akin to 'a flat out miracle is required to make life, generating life from non-life is in principle impossible for nature', I'd – to use chunkdz's words – throw him under a bus in an instant. But he's not. In fact, he is, and other ID proponents are, arguing something that seems markedly different from what you're rendering their words as. As near as I can tell, anyway.

    But anyway, we've been around this merry-go-round a few times in this thread already, I'm not really interested in arguing with people who take the obvious main points made by the ID leaders like Meyer, and then claim that they aren't saying those things at all.

    Well, Nick, all I can do is thank you for your input here. I may disagree with you – hell, I think you're doing grave injustice to what Meyer and company say (Why in the world do you keep going back to 'ID leaders'? You keep saying 'focus on Meyer' and then you take aim at this broader group) – but you were civil, you didn't stoop to namecalling, and you weren't a smug jackass. So again, thanks.

    But just to again say, I don't think what's "obvious" about the ID leaders is at all really "obvious". Just like, when I hear some ID critics yell about how Behe is "obviously" some closet YEC, I'm not going to grant it. It's not obvious at all. In fact, it seems dead wrong. In an obvious way.

    70. Comment by nullasalus — January 17, 2010 @ 2:43 am

  70. ID guy Says:
    January 17th, 2010 at 10:32 am

    computerist-

    The reply was to Nick and anyone else who wants to measure biological information:

    To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    71. Comment by ID guy — January 17, 2010 @ 10:32 am

  71. computerist Says:
    January 17th, 2010 at 11:04 am

    Hi IDGuy, no problem! :razz:

    72. Comment by computerist — January 17, 2010 @ 11:04 am

  72. Zachriel Says:
    January 17th, 2010 at 1:51 pm

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    Nylonase is about 400 amino acids, or 6*400 bits. Assuming random assembly and uniform distribution, the odds are roughly 1 in 10^720—way beyond the Universal Probabililty Bound.

    73. Comment by Zachriel — January 17, 2010 @ 1:51 pm

  73. ID guy Says:
    January 17th, 2010 at 6:59 pm

    Zachriel:
    Nylonase is about 400 amino acids, or 6*400 bits. Assuming random assembly and uniform distribution, the odds are roughly 1 in 10^720—way beyond the Universal Probabililty Bound.

    Why assume random assembly?

    Is there a reason for your post that you would wish to share?

    Dembski weighs in on nylonase

    new developments in nylon-eating :mrgreen:

    74. Comment by ID guy — January 17, 2010 @ 6:59 pm

  74. nickmatzke Says:
    January 17th, 2010 at 8:25 pm

    # ID guy Says:
    January 16th, 2010 at 10:36 am

    To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    Comment by ID guy — January 16, 2010

    Hey great. Well then, every time we have a gene duplication, and one of the copies is modified to a new function via mutation and selection — and there are numerous examples of this process occurring in nature — we have had an approximate doubling of the amount of information. And therefore Meyer's key claim is wrong, and it is actually easy for natural processes to create large amounts of new information, and therefore we cannot safely deduce intelligence from the existence of information. Game over for Meyer.

    75. Comment by nickmatzke — January 17, 2010 @ 8:25 pm

  75. ID guy Says:
    January 17th, 2010 at 9:53 pm

    nickmatzke:
    Well then, every time we have a gene duplication, and one of the copies is modified to a new function via mutation and selection — and there are numerous examples of this process occurring in nature — we have had an approximate doubling of the amount of information.

    And those examples are?

    Why wouldn't gene duplication followed by mutations for a new function, followed by proper expression of the new gene, be evidence for directed evolution? (See "Not By Chance" Spetner 1997)

    BTW Meyer is concerned with the ORIGIN of information.

    By calling on gene duplication you are starting with the very thing that needs to be explained in the first place.

    IOW Nick, the game is still on. You are in the wrong ball-park. :mrgreen:

    76. Comment by ID guy — January 17, 2010 @ 9:53 pm

  76. Mung Says:
    January 18th, 2010 at 3:19 am

    Nature as conceived by some – "blind, unguided" natural forces – are inferred as incapable. Or more specifically, "nature" is capable of certain things, but the fact that it's capable of them is good reason to infer that they're anything but blind or unguided. In fact, we should infer there's intelligence and agency at work.

    Anything "blind, unguided, natural forces" can do should be considered miraculous.

    77. Comment by Mung — January 18, 2010 @ 3:19 am

  77. Zachriel Says:
    January 18th, 2010 at 8:50 am

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    According to your calculation, there are ~2400 bits of CSI in nylonase. If the CSI exceeds 500 bits, then it is an unambiguous signature of design.

    78. Comment by Zachriel — January 18, 2010 @ 8:50 am

  78. ID guy Says:
    January 18th, 2010 at 10:26 am

    Zachriel:
    According to your calculation, there are ~2400 bits of CSI in nylonase. If the CSI exceeds 500 bits, then it is an unambiguous signature of design.

    Not my claculation.

    I said to COUNT nucleotides.

    You counted amino acids.

    Also I take it that you didn't read the the articles on the links I provided and that is bad form.

    Also the argument is about the ORIGIN of CSI.

    Nylonase came about after a very significant amount of CSI was present and operating.

    79. Comment by ID guy — January 18, 2010 @ 10:26 am

  79. Zachriel Says:
    January 18th, 2010 at 10:32 am

    ID guy: I said to COUNT nucleotides. You counted amino acids.

    There are three bases per amino acids. That means there are six bits per amino acid. If there are 400 amino acids, that means there are 1200 nucleotides or 2400 bits of CSI. That is per your calculation. Nylonase is a novel enzyme, and the CSI calculation leads to an unambiguous signal of design.

    80. Comment by Zachriel — January 18, 2010 @ 10:32 am

  80. ID guy Says:
    January 18th, 2010 at 10:44 am

    Zachriel:
    Nylonase is a novel enzyme…

    Novel, meaning it arose completely from scratch?

    Do you have evidence for that?

    However it appears that you still did not read the articles I linked to.

    Is that how you "debate"- by ignoring what other people post?

    Now I understand why you were banned from Uncommon Descent…

    81. Comment by ID guy — January 18, 2010 @ 10:44 am

  81. ID guy Says:
    January 18th, 2010 at 10:49 am

    Gene dupication-

    If I completely copy a dictionary do I now have twice the information?

    No.

    IOW gene dupication does not double the amount of information.

    And if a gene is dupicated and active all that is going to happen is another copy of an existing protein will be made.

    Hoepfully it doesn't get in the way of the already functioning machinery present.

    Then say that dupicated sequence gets mutated. Now we have a different protein roaming around the cell "looking" for something to do.

    Cross-reactions can occur- reactions tat would prevent the needed machinery from assembling or functioning.

    82. Comment by ID guy — January 18, 2010 @ 10:49 am

  82. Zachriel Says:
    January 18th, 2010 at 10:54 am

    ID guy: Novelmeaning it arose completely from scratch?

    The function is novel. But that's irrelevant to your calculation.

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    We have a biologically functioning system. "all you have to do is figure out what DNA sequence(s) are required to build it and count them," which in this case is 1200 bases, multiplied by 2, and we get 2400 bits of CSI.

    Are you now suggesting that your original statement was incorrect? That's fine. Just say so, and we can move on.

    83. Comment by Zachriel — January 18, 2010 @ 10:54 am

  83. ID guy Says:
    January 18th, 2010 at 10:58 am

    Novelmeaning it arose completely from scratch?

    Zachriel:
    The function is novel. But that's irrelevant to your calculation.

    Novel function has nothing to do with it.

    Did it arise from scratch?

    This debate is how did the information arise.

    And why are you ignoring the articles I linked to?

    Do you think that helps you in some way?

    Ignorance is never helpful.

    84. Comment by ID guy — January 18, 2010 @ 10:58 am

  84. Zachriel Says:
    January 18th, 2010 at 11:41 am

    ID guy: This debate is how did the information arise.

    Actually, you posted a calculation of information.

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    Every comment by Zachriel on this thread is directed towards that. According to your calculation, there are 2400 bits of CSI in nylonase. Are you now suggesting that your original statement was incorrect? That's fine. Just say so, and we can move on.

    85. Comment by Zachriel — January 18, 2010 @ 11:41 am

  85. ID guy Says:
    January 18th, 2010 at 5:01 pm

    Zachriel:
    Actually, you posted a calculation of information.

    I know what I posted.

    That does not change the debate which is about the origins of CSI.

    Zachriel:
    According to your calculation, there are 2400 bits of CSI in nylonase.

    Only if what you say about it is correct.

    You have to support that claim first.

    86. Comment by ID guy — January 18, 2010 @ 5:01 pm

  86. Zachriel Says:
    January 18th, 2010 at 5:32 pm

    ID guy: I know what I posted.

    Yes, and by your calculation, nylonase has about 2400 bits of CSI.

    ID guy: Only if what you say about it is correct.

    Kato et al., A plasmid encoding enzymes for nylon oligomer degradation, Microbiology 1995.

    87. Comment by Zachriel — January 18, 2010 @ 5:32 pm

  87. ID guy Says:
    January 18th, 2010 at 6:21 pm

    There isn't anything more recent than a paper from 1995?

    Just askin'

    BTW I am still waiting for the reason for your post about nylonase.

    If you don't want to say that is fine.

    Just count me out until you are ready to tell us.

    88. Comment by ID guy — January 18, 2010 @ 6:21 pm

  88. Zachriel Says:
    January 18th, 2010 at 6:41 pm

    ID guy: There isn't anything more recent than a paper from 1995?

    The paper give the length of nylonase as 392 amino acids. That was what was required for your calculation.

    ID guy: BTW I am still waiting for the reason for your post about nylonase.

    It's an example to plug into your calculation. The result was ~2400.

    89. Comment by Zachriel — January 18, 2010 @ 6:41 pm

  89. ID guy Says:
    January 18th, 2010 at 7:30 pm

    So there isn't anything more recent than the 1995 paper?

    Is there any reason you are ignoring the binding site and regulatory information?

    The point being is that the approximately 2400 bits would be a low end figure.

    90. Comment by ID guy — January 18, 2010 @ 7:30 pm

  90. ID guy Says:
    January 18th, 2010 at 7:51 pm

    3.Yasuhira, K. et al, 2007. 6-Aminohexanoate Oligomer Hydrolases from the Alkalophilic Bacteria Agromyes sp. Strain KY5R and Kocuria sp. Strain KY2. Applied and Environmental Microbiology. 73 (21): 7099-7102.

    It looks like a protein called EII- an existing protein- was altered by a mutation in its gene.

    EII has the ability to break down small circular proteins.

    Nylon is very protein-like.

    This looks like a loss of specification.

    91. Comment by ID guy — January 18, 2010 @ 7:51 pm

  91. Zachriel Says:
    January 18th, 2010 at 9:12 pm

    ID guy,

    All we're trying to do is calculate the CSI of nylonase per your comment above.

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits).

    If your instructions are not correct, and we have to account for the history of the sequence, then just say so and we'll move on. But there's nothing in those instructions concerning the history of the sequence.

    92. Comment by Zachriel — January 18, 2010 @ 9:12 pm

  92. ID guy Says:
    January 18th, 2010 at 9:42 pm

    Zachriel:
    All we're trying to do is calculate the CSI of nylonase per your comment above.

    Context is important.

    I tried to help you out with that but it appears you wish to force your will- mistaken as it may be- into the discussion.

    Zachriel:
    If your instructions are not correct, and we have to account for the history of the sequence, then just say so and we'll move on.

    Well I sure as hell didn't provide those instructions in a vacuum.

    There was a discussion going on and context presented.

    Now sure that alone doesn't prevent some butthead from wandering into a discussion and blindly flail about.

    Zachriel:
    But there's nothing in those instructions concerning the history of the sequence.

    There is a history behind what I said- ie a context.

    Now I understand why context doesn't concern you because all you are concerned with is obfuscation.

    IOW there was a good reason why you were banned from Uncommon Descent- again.

    Geez they keep giving you oppportunity after opportunity yet you just post the same obfuscation.

    93. Comment by ID guy — January 18, 2010 @ 9:42 pm

  93. ID guy Says:
    January 18th, 2010 at 9:51 pm

    Third comment Zachriel:

    olegt:
    (1) define what you mean by information in the genome and (2) tell us how you would measure its amount in practice.

    My answer:

    To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits). (biological function being what we mean by information in a genome)

    Next, in context, it is about origins, as in "how did this come into existence?"- meaning its history.

    So what the #$@! is your problem?

    Or will you not share that with us? :mrgreen:

    94. Comment by ID guy — January 18, 2010 @ 9:51 pm

  94. Zachriel Says:
    January 18th, 2010 at 10:45 pm

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits). (biological function being what we mean by information in a genome)

    You just repeated the instructions. So, according to that, nylonase has ~2400 bits of CSI.

    ID guy: Next, in context, it is about origins, as in "how did this come into existence?"- meaning its history.

    At this point, we are attempting an unambiguous calculation of information. Is the calculation correct, or are the instructions wrong?

    95. Comment by Zachriel — January 18, 2010 @ 10:45 pm

  95. nickmatzke Says:
    January 19th, 2010 at 3:14 am

    And those examples are?

    Right here: Long et al. (2003), "The origin of new genes: glimpses from the young and old." Nature Reviews Genetics.

    BTW Meyer is concerned with the ORIGIN of information.

    By calling on gene duplication you are starting with the very thing that needs to be explained in the first place.

    No, it is Meyer that makes a very strong generalizations: only intelligence can create new information. His whole argument relies on the idea that *only* intelligence can do this. So we are trying to get a quantifiable definition, so we can test that claim.

    On your definition of information, Meyer's generalization is clearly false.

    IOW Nick, the game is still on. You are in the wrong ball-park.

    You're not even playing the right sport. [/pulp fiction]

    Moving on:

    If I completely copy a dictionary do I now have twice the information?

    No.

    IOW gene dupication does not double the amount of information.

    And if a gene is dupicated and active all that is going to happen is another copy of an existing protein will be made.

    Agreed so far.

    Then say that dupicated sequence gets mutated. Now we have a different protein roaming around the cell "looking" for something to do.

    Wow. You just admitted we have a different, new protein! I.e., new information.

    Cross-reactions can occur- reactions tat would prevent the needed machinery from assembling or functioning.

    Sure, cross-reactions will sometimes occur, and the new protein will not be beneficial. It will thus be selected against, and it will never spread throughout the population.

    But in order for Meyer's generalization to be true, you have to show that the duplicated, mutated new protein will NEVER, EVER be beneficial, despite lots of evidence that sometimes they can be and have been beneficial. Additionally, you have to show that every one of the 22 examples of new genes, shown in Table 1 of Long et al. 2003, is a mistaken analysis by scientists. (And all of the additional examples published since then.)
    Until you do that, we have won the argument, and Meyer's key generalization, the one upon which his whole argument rests, is wrong.

    96. Comment by nickmatzke — January 19, 2010 @ 3:14 am

  96. ID guy Says:
    January 19th, 2010 at 8:04 am

    Nick,

    The debate has alwatys been about the ORIGIN of CSI- ALWAYS.

    So if you start with that which needs to be explained in the first place- living organisms- then you lose.

    That you refuse to understand that just proves you don't care about representing reality.

    97. Comment by ID guy — January 19, 2010 @ 8:04 am

  97. ID guy Says:
    January 19th, 2010 at 8:10 am

    Nick,

    In order for your "argument" to have any merit you must show that gene duplication followed by a function-altering mutation is blind and non-goal oriented.

    And the only way to do that- that I am aware of- is to show that living organisms can be reduced to those types of processes.

    The debate is about what blind and non-goal oriented processes can do Nick.

    That is it, period, end of story.

    98. Comment by ID guy — January 19, 2010 @ 8:10 am

  98. ID guy Says:
    January 19th, 2010 at 8:12 am

    Zachriel:
    You just repeated the instructions. So, according to that, nylonase has ~2400 bits of CSI.

    Why are you ignoring the other information?

    At this point, we are attempting an unambiguous calculation of information. Is the calculation correct, or are the instructions wrong?

    I don't care what you are doing.

    The calculation is wrong and I told you why.

    99. Comment by ID guy — January 19, 2010 @ 8:12 am

  99. ID guy Says:
    January 19th, 2010 at 8:17 am

    Nick,

    All your position has are generalizations.

    Just sayin'

    100. Comment by ID guy — January 19, 2010 @ 8:17 am

  100. Zachriel Says:
    January 19th, 2010 at 8:34 am

    Zachriel: You just repeated the instructions. So, according to that, nylonase has ~2400 bits of CSI.

    ID guy: Why are you ignoring the other information?

    We're looking for a straight answer. The calculation is based on your repeated instructions. Does nylonase have ~2400 bits of CSI?

    101. Comment by Zachriel — January 19, 2010 @ 8:34 am

  101. ID guy Says:
    January 19th, 2010 at 8:43 am

    Why are you ignoring the other information?

    IOW Zachriel you are not following my instructions.

    So what is your problem?

    Do you understand English?

    102. Comment by ID guy — January 19, 2010 @ 8:43 am

  102. Zachriel Says:
    January 19th, 2010 at 8:44 am

    ID guy: The calculation is wrong and I told you why.

    Oh? Here are your instructions:

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits). (biological function being what we mean by information in a genome)

    Nylonase is a functional biological enzyme. The protein has ~400 amino acids. At one codon per amino acid, three bases per codon, and two bits per base, that's ~2400 bits of CSI. Now you say the calculation is wrong, even though it is based on your own instructions. So are you saying those instructions are not correct? If so, say so and we can move on.

    103. Comment by Zachriel — January 19, 2010 @ 8:44 am

  103. Zachriel Says:
    January 19th, 2010 at 8:53 am

    ID guy: All your position has are generalizations.

    Actually, nickmatzke cited a paper with specifics on the origin of new genes, including recent arrivals that reveal new mechanisms of evolutionary variation (e.g. exon shuffling). Here's a few more specifics:

    Okamura et al., Frequent appearance of novel protein-coding sequences by frameshift translation, Genomics 2006.

    104. Comment by Zachriel — January 19, 2010 @ 8:53 am

  104. ID guy Says:
    January 19th, 2010 at 9:19 am

    The calculation is wrong and I told you why.

    Zachriel:
    Oh? Here are your instructions:

    To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits). (biological function being what we mean by information in a genome)

    That is right and you are not following them.

    Why is that?

    I even explained it to you and you are still ignorant.

    So what is your porblem?

    105. Comment by ID guy — January 19, 2010 @ 9:19 am

  105. ID guy Says:
    January 19th, 2010 at 9:20 am

    Actually nickmatzke linked to a paper rife with generalizations.

    106. Comment by ID guy — January 19, 2010 @ 9:20 am

  106. Zachriel Says:
    January 19th, 2010 at 9:26 am

    ID guy: That is right and you are not following them.

    Okay, showing your work and following your instructions, please calculate the CSI of nylonase.

    107. Comment by Zachriel — January 19, 2010 @ 9:26 am

  107. Zachriel Says:
    January 19th, 2010 at 9:31 am

    ID guy: Actually nickmatzke linked to a paper rife with generalizations.

    You might want to actually read the citations included with the paper which is where you'll find the specifics in a scientific review. For more specifics, don't forget the paper on frameshifts.

    Long et al., The origin of new genes: glimpses from the young and old, Nature Reviews Genetics 2003.

    Okamura et al., Frequent appearance of novel protein-coding sequences by frameshift translation, Genomics 2006.

    108. Comment by Zachriel — January 19, 2010 @ 9:31 am

  108. ID guy Says:
    January 19th, 2010 at 9:39 am

    Zachriel,

    The theory of evolution is all about generalizations.

    You have even admitted that its pretense to non-telic processes is not scientific.

    As for calculating the information in nylonase- no thanks that is your issue, not mine.

    However it is obvious that you cannot even understand English.

    IOW information is useless to Zachriel.

    109. Comment by ID guy — January 19, 2010 @ 9:39 am

  109. Zachriel Says:
    January 19th, 2010 at 10:05 am

    ID guy: As for calculating the information in nylonase- no thanks that is your issue, not mine.

    As everyone can see, ID guy is unable or unwilling to calculate a simple example, or to follow his own simple instructions to determine a result.

    110. Comment by Zachriel — January 19, 2010 @ 10:05 am

  110. ID guy Says:
    January 19th, 2010 at 12:28 pm

    As everyone can see Zachriel cannot follow simple instructions and now wants me to do his work for him.

    111. Comment by ID guy — January 19, 2010 @ 12:28 pm

  111. ID guy Says:
    January 19th, 2010 at 12:35 pm

    To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits). (biological function being what we mean by information in a genome)

    HINT (again)- The DNA sequence(s) required to build it is greater than the sequence portrayed by the amino acid sequence

    AsI said yesterday @ 7:30 PM:

    The point being is that the approximately 2400 bits would be a low end figure.

    You can either understand that and move on or ignore it and move on.

    I just want you to know that you did not follow my instructions, but you do seem to be able to do the basic math required.

    You just need to calm down and get to all the information, not just the resulting protein.

    112. Comment by ID guy — January 19, 2010 @ 12:35 pm

  112. ID guy Says:
    January 19th, 2010 at 12:39 pm

    bump…

    nickmatzke:
    On your definition of information, Meyer's generalization is clearly false.

    Only if you cheat by starting with that which needs to be explained in the first place.

    113. Comment by ID guy — January 19, 2010 @ 12:39 pm

  113. Zachriel Says:
    January 19th, 2010 at 12:57 pm

    ID guy: The point being is that the approximately 2400 bits would be a low end figure.

    You're saying that nylonase is not a "biologically functioning system," even though it breaks down nylon. So, we can't calculate the CSI of nylonase, but only of the entire bacteria, including its environment. Or where do you draw the line?

    114. Comment by Zachriel — January 19, 2010 @ 12:57 pm

  114. ID guy Says:
    January 19th, 2010 at 1:09 pm

    The point being is that the approximately 2400 bits would be a low end figure.

    Zachriel:
    You're saying that nylonase is not a "biologically functioning system," even though it breaks down nylon.

    No. That doesn't even follow from what I said.

    IOW that is a pure fabrication on your part.

    What I am saying is that you are incapable of following simple instructions.

    I am also saying that you are an obtuse jerk- that is what the evidence points to- just sayin'

    Zachriel:
    So, we can't calculate the CSI of nylonase,

    The people who can follow instructions should be able to.

    You seemed to have figured out the lowest number of bits required. So that is a start.

    So now that you have that low-end number what next?

    115. Comment by ID guy — January 19, 2010 @ 1:09 pm

  115. ID guy Says:
    January 19th, 2010 at 1:21 pm

    If nylonase evolved from EII, and EII has more amino acids and therefor more information (given the same meta-information), then is nylonase an example of information gain or loss? :mrgreen:

    116. Comment by ID guy — January 19, 2010 @ 1:21 pm

  116. Zachriel Says:
    January 19th, 2010 at 1:25 pm

    ID guy: That doesn't even follow from what I said.

    There are seven lines in your comment, and not one addressed the question.

    If nylonase is a "biologically functioning system," then we should be able to measure its CSI per the definition.

    ID guy: To measure the information in a biologically functioning system all you have to do is figure out what DNA sequence(s) are required to build it and count them- 2 bits per nucleotide (4 nucleotides = 2^2, which means 2 bits). (biological function being what we mean by information in a genome)

    Most people would take the "what DNA sequence(s) are required to build it" to mean the sequence that codes for the system. But if you are indicating it has to include other aspects of the genome involved in translation, then you should simply say so, and provide the relevant calculations. But you can't build it from nothing, so it has to include the mechanism which delivers resources to the mechanism. In fact, it could entail the entire organism, and the organism's environment, including all the other organisms in that environment. And so on.

    But you seem incapable of provide us a precise answer. Can you show us how to use your instructions to calculate the CSI of nylonase? Where do we draw the line as to what constitutes what is "required to build" the system?

    ID guy: If nylonase evolved from EII, and EII has more amino acids and therefor more information (given the same meta-information), then is nylonase an example of information gain or loss?

    No way to tell until you can decide what you mean by information.

    117. Comment by Zachriel — January 19, 2010 @ 1:25 pm

  117. ID guy Says:
    January 19th, 2010 at 1:37 pm

    Zachriel:
    If nylonase is a "biologically functioning system," then we should be able to measure its CSI per the definition.

    Instructions- and yes if you follow them.

    The low-end number you provided is fine.

    What did you want to do with it?

    Most people would take the "what DNA sequence(s) are required to build it" to mean the sequence that codes for the system.

    If that is what I wanted to mean then that is what I would have said.

    However most people who understand biology understand that there is more to it than that.

    The whole debate is about how that information came to be.

    and

    If nylonase evolved from EII, and EII has more amino acids and therefor more information (given the same meta-information), then is nylonase an example of information gain or loss?

    No way to tell until you can decide what you mean by information.

    I have decided. I put it in writing. That you choose to be obtuse is not my problem.

    118. Comment by ID guy — January 19, 2010 @ 1:37 pm

  118. ID guy Says:
    January 19th, 2010 at 1:45 pm

    The debate is about the origin of CSI- biological functionality.

    If stereochemical processes can account for the origin of living organisms then CSI doesn't exist and any discussion of nylonase is moot.

    And if living organisms are the result of Intelligent Design then nylonase would be a case for Dr Spetner's position laid out in "Not By Chance".

    119. Comment by ID guy — January 19, 2010 @ 1:45 pm

  119. Zachriel Says:
    January 19th, 2010 at 2:06 pm

    So you've put a lower bound on the information content of nylonase, but can't put an upper bound, or even a means for determining the upper bound. Is that correct?

    ID guy: The debate is about the origin of CSI- biological functionality.

    Nylonase evolved through mutation, yet has at least 2400 bits of CSI.

    120. Comment by Zachriel — January 19, 2010 @ 2:06 pm

  120. ID guy Says:
    January 19th, 2010 at 2:16 pm

    Zachriel:
    So you've put a lower bound on the information content of nylonase, but can't put an upper bound, or even a means for determining the upper bound. Is that correct?

    That is incorrect.

    I told you how to do it.

    I never said it was easy.

    I know it takes research.

    The debate is about the origin of CSI- biological functionality.

    Zachriel:
    Nylonase evolved through mutation, yet has at least 2400 bits of CSI.

    That doesn't say anything about whether or not the mutation was blind and non-goal oriented or was direcetd by the cells internal program- as Dr Spetner said.

    But yes it appears the mutation decreased the amount of information that was present before.

    Is that what you were shooting for- an information decreasing mutation?

    121. Comment by ID guy — January 19, 2010 @ 2:16 pm

  121. Zachriel Says:
    January 19th, 2010 at 2:21 pm

    ID guy: I told you how to do it.

    Then you won't mind providing a step-by-step calculation based on your instructions.

    ID guy: But yes it appears the mutation decreased the amount of information that was present before.

    You can't determine that until you have an unambiguous measure of the information.

    122. Comment by Zachriel — January 19, 2010 @ 2:21 pm

  122. ID guy Says:
    January 19th, 2010 at 2:30 pm

    Zachriel:
    You can't determine that until you have an unambiguous measure of the information.

    I provided exactly that.

    Your personal problems do not reflect on my instructions.

    123. Comment by ID guy — January 19, 2010 @ 2:30 pm

  123. ID guy Says:
    January 19th, 2010 at 2:35 pm

    If nylonase evolved from EII, and EII has more amino acids and therefor more information (given the same meta-information), then is nylonase an example of information gain or loss?

    Notice the caveat (given the same meta-information).

    The caveat that Zachriel either ignored or couldn't comprehend.

    So given the same meta-information it is clear that nylonase is a decrease of information in comparison to EII.

    Is that what you were shooting for Zach? Really?

    124. Comment by ID guy — January 19, 2010 @ 2:35 pm

  124. Zachriel Says:
    January 19th, 2010 at 8:22 pm

    ID guy: I provided exactly that.

    Oh? What is the CSI of nylonase? For some reason, you introduced a new and undefined term, "meta-information."

    125. Comment by Zachriel — January 19, 2010 @ 8:22 pm

  125. ID guy Says:
    January 20th, 2010 at 8:01 am

    If nylonase evolved from EII, and EII has more amino acids and therefor more information (given the same meta-information), then is nylonase an example of information gain or loss?

    Thanks Zach… :mrgreen:

    126. Comment by ID guy — January 20, 2010 @ 8:01 am

  126. Zachriel Says:
    January 20th, 2010 at 8:29 am

    ID guy: If nylonase evolved from EII, and EII has more amino acids and therefor more information (given the same meta-information), then is nylonase an example of information gain or loss?

    Apparently, you can't provide a valid definition of information, much less quantify "meta-information."

    127. Comment by Zachriel — January 20, 2010 @ 8:29 am

  127. ID guy Says:
    January 20th, 2010 at 8:43 am

    Apparently you are just too obtuse to understand anything.

    Why do you think your issues are a reflection on my comments?

    BTW meta-information has been defined and introduced.

    IOW Zach you are once again trying to argue from ignorance.

    Do you think that helps you?

    I also take it that it upsets you that your example shows that mutations can cause a loss of information- by any standard.

    128. Comment by ID guy — January 20, 2010 @ 8:43 am

  128. Zachriel Says:
    January 20th, 2010 at 8:59 am

    ID guy: Apparently you are just too obtuse to understand anything.

    The question is very simple. Based on your instructions, show us how to work out the CSI of nylonase. Can you use your instructions to calculate the "meta-information?" Or are you saying your instructions are wrong?

    ID guy: I also take it that it upsets you that your example shows that mutations can cause a loss of information- by any standard.

    There's no way to justify that claim if you can't provide an unambiguous metric for information. If the original gene duplicated, then mutated, that would leave the original function intact, while adding a new function. Or the meta-world may change when the new gene evolves, such as how mitochondria are posited to have transferred some of their functions to the nucleus.

    -
    What is amazing is that such poor arguments are never challenged within the ID Community. Errors are corrected among the scientific community—even simple ones. It's part of the charm of intellectual life. (And one can learn more from mistakes, if willing, than from blathering about what one already knows.) But here we have someone who claims a simple rule to calculate a fundamental quantity in ID Science, and yet can't give an unambiguous result. It looks a lot like Shannon Information, only it's not—apparently.

    Can we calculate the CSI of nylonase? Or is CSI undefined for nylonase? If so, can it only be determined within the context of so-called meta-information? If so, how can we calculate meta-information? What is encompassed in meta-information? Protein synthesis? What about the necessary materials? Don't we need to include the whole cell? How it acquires resources? It's behavior? The cell and its environment, including other organisms, including through time, through all time? If we do, then the meta-information of every thing is the information of Everything.

    129. Comment by Zachriel — January 20, 2010 @ 8:59 am

  129. ID guy Says:
    January 20th, 2010 at 9:25 am

    Zachriel:
    Errors are corrected among the scientific community—even simple ones.

    You make the error of Common Descent expecting a nested hierarchy all the time.

    You have been corrected many times now.

    Yet you don't seem to be able to correct your position.

    130. Comment by ID guy — January 20, 2010 @ 9:25 am

  130. ID guy Says:
    January 20th, 2010 at 11:23 am

    Back to nylonase:

    Zachriel:
    Nylonase evolved through mutation, yet has at least 2400 bits of CSI.

    What do you mean by "yet"?

    No one is saying that something cannot evolve through mutation*.

    As I said it appears said mutation decreased the specified information, meaning the new product has less specified information than the "parent".

    And that it evolved under severe selection it appears to provide support for Dr Spetner's hypothesis.

    *the debate is about what blind, non-goal oriented processes can do – we already know that intellignet agencies can produce vast amounts of specified information.

    131. Comment by ID guy — January 20, 2010 @ 11:23 am

  131. Zachriel Says:
    January 20th, 2010 at 12:11 pm

    ID guy: As I said it appears said mutation decreased the specified information, meaning the new product has less specified information than the "parent".

    Again, there's no way to support that claim without an unambiguous metric for what you are calling information. Can you provide that?

    For others following the thread. It appears that ID guy has set a lower-bound of 6*392 = 2352 bits. Of course, that's not a very accurate lower-bound. For instance, we can show that the amount of Shannon Information is less than 5 bits per amino acid. So now that lower-bound is, well, lower. Also, if some of the protein is redundant or non-essential, then that would lower the lower-bound some more.

    132. Comment by Zachriel — January 20, 2010 @ 12:11 pm

  132. ID guy Says:
    January 20th, 2010 at 12:43 pm

    Zachriel:
    Again, there's no way to support that claim without an unambiguous metric for what you are calling information.

    Then we are at an impasse.

    I say I have provided an unambiguous metric.

    I say that you are the problem, not my instructions.

    So in order to clear this up perhaps you can provide an unambiguous metric for the alleged evolution of the whale from a land animal via blind, non-goal oriented processes.

    That way I will understand exactly what you will accept.

    It appears that ID guy has set a lower-bound of 6*392 = 2352 bits.

    You did that.

    Of course, that's not a very accurate lower-bound.

    Sure it is- that is if your information is correct.

    For instance, we can show that the amount of Shannon Information is less than 5 bits per amino acid.

    Why- because there are 20 amino acids plus a stop (sign)- but they can be coded by 64 different codons (2^6).

    And that is why I said count the nucleotides.

    So now that lower-bound is, well, lower.

    Not if you follow my instructions.

    Also, if some of the protein is redundant or non-essential, then that would lower the lower-bound some more.

    Again this all depends on the accuracy of the information Zachriel provided.

    All I have is what you said.

    133. Comment by ID guy — January 20, 2010 @ 12:43 pm

  133. Zachriel Says:
    January 20th, 2010 at 1:41 pm

    ID guy: Then we are at an impasse.

    Yes, that's been apparent for some time.

    By the way, the Shannon Information in proteins based on the observed distribution of amino acids is just 4.18 bits per residue.

    134. Comment by Zachriel — January 20, 2010 @ 1:41 pm

  134. ID guy Says:
    January 20th, 2010 at 2:08 pm

    Yes it has been apparent for some time that you are the problem.

    So in order to clear this up perhaps you can provide an unambiguous metric for the alleged evolution of the whale from a land animal via blind, non-goal oriented processes.

    That way I will understand exactly what you will accept.

    135. Comment by ID guy — January 20, 2010 @ 2:08 pm

  135. ID guy Says:
    January 20th, 2010 at 2:14 pm

    Zachriel:
    By the way, the Shannon Information in proteins based on the observed distribution of amino acids is just 4.18 bits per residue.

    Why just proteins?

    Why not include every possible amino acid sequence seeing that Shannon doesn't give a rat's butt about functionality?

    It appears that you are selectively applying Shannon.

    There isn't any differnce in Shannon information between a 392 amino-acid chain (polypeptide) that functions as a nylon degrader and a 392 amino-acid chain (polypeptide) that won't even fold.

    136. Comment by ID guy — January 20, 2010 @ 2:14 pm

  136. Zachriel Says:
    January 20th, 2010 at 2:43 pm

    ID guy: It appears that you are selectively applying Shannon.

    Nope. Shannon Information is a well-defined theory of information. We're trying to get an unambiguous metric of CSI.

    ID guy: There isn't any differnce in Shannon information between a 392 amino-acid chain (polypeptide) that functions as a nylon degrader and a 392 amino-acid chain (polypeptide) that won't even fold.

    That's correct.

    ID guy: Why not include every possible amino acid sequence seeing that Shannon doesn't give a rat's butt about functionality?

    There are 64 codons, but only 20 or so amino acids. If we assume a uniform distribution of amino acids, then there are about 4½ bits per amino acid.

    137. Comment by Zachriel — January 20, 2010 @ 2:43 pm

  137. ID guy Says:
    January 20th, 2010 at 3:00 pm

    It appears that you are selectively applying Shannon.

    Zachriel:
    Nope. Shannon Information is a well-defined theory of information.

    Meyer talks about Shannon's theory in "Signature in the Cell".

    The word information in this theory is used in a special mathematical sense that must not be confused with its ordinary usage. In particular, information must not be confused with meaning. Warren Weaver- collaborated with Shannon

    IOW as Meyer explains Shannon only deals with mere complexity/ information carrying capacity.

    Why not include every possible amino acid sequence seeing that Shannon doesn't give a rat's butt about functionality?

    There are 64 codons, but only 20 or so amino acids.

    The STOP codon. You forgot the STOP codon.

    Also you are still missing the point.

    I said to count the nucleotides.

    You, being the obtuse jerk that you are, switched it to amino acids using 6 bits per amino acid.

    Now you want to change that.

    One thing for certain no one can figure out the number of bits if you keep changing the criteria.

    However all of that could have been avoided had you just followed my instructions in the first place.

    So I thank you for proving my point- you were the problem all along.

    138. Comment by ID guy — January 20, 2010 @ 3:00 pm

  138. ID guy Says:
    January 20th, 2010 at 3:02 pm

    If we assume a uniform distribution of amino acids, then there are about 4½ bits per amino acid.

    How does one transmit "about a half of bit"?

    I am pretty sure Shannon was concerned with the transmission and storage of bits.

    Did he discuss 1/2 bit transmission and storage?

    139. Comment by ID guy — January 20, 2010 @ 3:02 pm

  139. Zachriel Says:
    January 20th, 2010 at 3:07 pm

    Zachriel: There are 64 codons, but only 20 or so amino acids.

    ID guy: The STOP codon. You forgot the STOP codon.

    There are 64 codons.

    ID guy: I said to count the nucleotides.

    That's fine. So the CSI of nylonase is defined by its gene sequence plus a stop codon, which represents about 2400 bits. So the CSI of nylonase is about 2400 bits. Is that correct?

    140. Comment by Zachriel — January 20, 2010 @ 3:07 pm

  140. ID guy Says:
    January 20th, 2010 at 3:09 pm

    Zachriel,

    I take it that you are not going to provide an unambiguous metric for the alleged evolution of the whale from a land animal via blind, non-goal oriented processes.

    Is there any way to quantify anything in the present theory of evolution?

    141. Comment by ID guy — January 20, 2010 @ 3:09 pm

  141. ID guy Says:
    January 20th, 2010 at 3:12 pm

    Zachriel:
    There are 64 codons.

    Only 61 of which match with an amino acid.

    I said to count the nucleotides.

    Zachriel:
    That's fine. So the CSI of nylonase is defined by its gene sequence plus a stop codon, which represents about 2400 bits. So the CSI of nylonase is about 2400 bits. Is that correct?

    Correct enough for a lazy, careless person I guess.

    Is there a binding site involved?

    How many nucleotides is it?

    142. Comment by ID guy — January 20, 2010 @ 3:12 pm

  142. Zachriel Says:
    January 20th, 2010 at 3:17 pm

    ID guy: Did he discuss 1/2 bit transmission and storage?

    Yes, of course. For instance, Shannon said "a decimal digit is about 3 1/3
    bits."

    Shannon, A Mathematical Theory of Communication, The Bell System Technical Journal 1948.

    143. Comment by Zachriel — January 20, 2010 @ 3:17 pm

  143. ID guy Says:
    January 20th, 2010 at 3:36 pm

    Zachriel:
    For instance, Shannon said "a decimal digit is about 3 1/3
    bits."

    Using Base 10.

    However binary digits- bits- use base 2.

    144. Comment by ID guy — January 20, 2010 @ 3:36 pm

  144. ID guy Says:
    January 20th, 2010 at 3:39 pm

    Typical Zachriel bait-n-switch-

    I asked:

    Did he discuss 1/2 bit transmission and storage?

    Bit means BINARY DIGIT base 2

    Zach responds with:

    For instance, Shannon said "a decimal digit is about 3 1/3
    bits."

    A decimal digit, base 10, is not a binary digit.

    Seeing that you are a spokes-person for the theory of evolution I want to thank you for continuing to show how empty your position is.

    145. Comment by ID guy — January 20, 2010 @ 3:39 pm

  145. Zachriel Says:
    January 20th, 2010 at 3:40 pm

    Zachriel: So the CSI of nylonase is about 2400 bits. Is that correct?

    ID guy: Correct enough for a lazy, careless person I guess. Is there a binding site involved?

    Nylonase is an enzyme that binds and hydrolyzes nylon byproducts.

    146. Comment by Zachriel — January 20, 2010 @ 3:40 pm

  146. ID guy Says:
    January 20th, 2010 at 3:43 pm

    Zachriel:
    Nylonase is an enzyme that binds and hydrolyzes nylon byproducts.

    And your point is?

    147. Comment by ID guy — January 20, 2010 @ 3:43 pm

  147. Zachriel Says:
    January 20th, 2010 at 3:54 pm

    ID guy: Bit means BINARY DIGIT base 2

    Yes.

    Zachriel: For instance, Shannon said "a decimal digit is about 3 1/3 bits."

    ID guy: A decimal digit, base 10, is not a binary digit.

    Transmitting a decimal digit requires about 3 1/3 binary digits (bits).

    ID guy: Did he discuss 1/2 bit transmission and storage?

    If you read his paper, there are fractional bits throughout.

    148. Comment by Zachriel — January 20, 2010 @ 3:54 pm

  148. ID guy Says:
    January 20th, 2010 at 4:11 pm

    Yes you can represent base 10 as fractions of a bit, but how do you transmit it?

    Say I wanted to send one decimal digit in binary, ie bits- what would the sequence look like, in 1s and 0s?

    149. Comment by ID guy — January 20, 2010 @ 4:11 pm

  149. ID guy Says:
    January 20th, 2010 at 4:12 pm

    Back to:

    Nylonase is an enzyme that binds and hydrolyzes nylon byproducts.

    Great. Case closed then.

    Good job.

    Thanks.

    150. Comment by ID guy — January 20, 2010 @ 4:12 pm

  150. ID guy Says:
    January 21st, 2010 at 8:30 am

    So we have nylonase with 392 amino acids and a stop codon.

    The protein it evolved from has over 400 amino acids and a stop codon.

    If more than 400 is greater than 392 then nylonase is a lose of information.

    Again is that what you were shooting for Zachriel?

    151. Comment by ID guy — January 21, 2010 @ 8:30 am

  151. Zachriel Says:
    January 21st, 2010 at 10:02 am

    ID guy: So we have nylonase with 392 amino acids and a stop codon.

    No. Nylonase does not have a stop codon. The gene that codes for nylonase has a stop codon.

    Thought the case was closed. All we want to know are the steps for calculating the CSI of nylonase, and what is the result. Is it 392*6+6?

    152. Comment by Zachriel — January 21, 2010 @ 10:02 am

  152. ID guy Says:
    January 21st, 2010 at 10:09 am

    Zachriel:
    Thought the case was closed.

    It is closed- nylonase is a clear case of information loss.

    Is that what you were shooting for- information losing mutations?

    153. Comment by ID guy — January 21, 2010 @ 10:09 am

  153. Zachriel Says:
    January 21st, 2010 at 10:21 am

    ID guy: Say I wanted to send one decimal digit in binary, ie bits- what would the sequence look like, in 1s and 0s?

    It depends, but you might transmit it as an 8-bit byte or a 16-bit word. It still constitutes about 3 1/3 bits of information. Consider an 8-bit byte and knowing that we are receiving a decimal number encoded with the least significant digit in the eighth digit. The first four digits are always zero, so they don't transmit any information. That's an important clue!

    Try to grasp that before continuing. It has to do with surprisal. There's no surprise in the first four digits. We already know they're zero before we even power up the receiver. They contain zero Shannon Information. Now, here's the fifth through eighth digits:


    0 - 0000
    1 - 0001
    2 - 0010
    3 - 0011
    4 - 0100
    5 - 0101
    6 - 0110
    7 - 0111
    8 - 1000
    9 - 1001

    The fifth digit is normally zero, but sometimes one. (It will be zero when the decimal digit is 0, 1, 2, 3, 4, 5, 6, 7, but one when the decimal digit is 8 or 9. The sixth digit will be zero when the decimal digit is 0, 1, 2, 3, 8, 9, but one when the decimal digit is 4, 5, 6, 7. The seventh digit will be zero when the decimal digit is 0, 1, 4, 5, 8, 9, but one when the decimal digit is 2, 3, 6, 7. The eight digit will be zero when the decimal digit is 0, 2, 4, 6, 8, but one when the decimal digit is 1, 3, 5, 7, 9.

    Only the eighth digit carries a full bit of information. The other bits are biased. (This bias can be used to compress the data.) Consequently, the Shannon Information of decimal digits is log2(10) bits.

    Hope that helps.

    154. Comment by Zachriel — January 21, 2010 @ 10:21 am

  154. Zachriel Says:
    January 21st, 2010 at 10:22 am

    Zachriel: All we want to know are the steps for calculating the CSI of nylonase, and what is the result. Is it 392*6+6?

    ID guy: nylonase is a clear case of information loss

    You didn't answer the question. If you don't know the answer, that's okay. Just say so. If your instructions for calculating CSI were wrong, that's okay too. Just say so and we can move on.

    155. Comment by Zachriel — January 21, 2010 @ 10:22 am

  155. ID guy Says:
    January 21st, 2010 at 10:46 am

    Yes you can represent base 10 as fractions of a bit, but how do you transmit it?

    Say I wanted to send one decimal digit in binary, ie bits- what would the sequence look like, in 1s and 0s?

    You didn't even address the question.

    How does one transmit a FRACTION of a bit?

    You responded by transmitting numerous bits.

    156. Comment by ID guy — January 21, 2010 @ 10:46 am

  156. ID guy Says:
    January 21st, 2010 at 10:52 am

    Zachriel:
    All we want to know are the steps for calculating the CSI of nylonase, and what is the result.

    I told you how to measure specified information in biology.

    You don't seem to understand those instructions.

    First you used amino acids and then started complaining that the amino acid to bit configuration you used was actually wrong.

    I then pointed out that is why I said to count nucleotides.

    I also said that the gene responsible for nylonase has to have a binding site.

    I asked how many nucleotides that binding site has.

    You responded by telling me what nylonase does.

    All along the way I have pointed out that nylonase has less information then what it evolved from.

    You just hand-wave that away.

    So what we have is Zachriel's failure to follow instructions and him projecting his shortcomings onto my instructions.

    157. Comment by ID guy — January 21, 2010 @ 10:52 am

  157. Zachriel Says:
    January 21st, 2010 at 10:52 am

    ID guy: Yes you can represent base 10 as fractions of a bit, but how do you transmit it?

    We used the example of transmitting decimal digits with 8-bit bytes.

    0 - 00000000
    1 - 00000001
    2 - 00000010
    3 - 00000011
    4 - 00000100
    5 - 00000101
    6 - 00000110
    7 - 00000111
    8 - 00001000
    9 - 00001001

    Read the explanation above and then answer how much Shannon Information is transmitted by the first bit (which is always zero)?

    158. Comment by Zachriel — January 21, 2010 @ 10:52 am

  158. ID guy Says:
    January 21st, 2010 at 10:55 am

    Zachriel,

    How does one transmit a fraction of a bit?

    159. Comment by ID guy — January 21, 2010 @ 10:55 am

  159. ID guy Says:
    January 21st, 2010 at 10:58 am

    8-bit bytes.

    Is there any other type of byte?

    I am pretty sure all bytes are 8 bits.

    However I have noticed that you have failed to show how to transmit a fraction of a bit.

    160. Comment by ID guy — January 21, 2010 @ 10:58 am

  160. ID guy Says:
    January 21st, 2010 at 11:00 am

    Zachriel:
    Read the explanation above and then answer how much Shannon Information is transmitted by the first bit (which is always zero)?

    One bit-

    Shannon doesn't care about value- so if a bit is transmitted then that bit is one bit, even if that bit is a zero.

    161. Comment by ID guy — January 21, 2010 @ 11:00 am

  161. Zachriel Says:
    January 21st, 2010 at 11:23 am

    ID guy: Shannon doesn't care about value- so if a bit is transmitted then that bit is one bit, even if that bit is a zero.

    The Shannon Information is the reduction in uncertainty due to receipt of the message (given a noiseless channel and based on the ensemble of all possible messages). In our example, that means the first four digits have no information as we already know what they are *before* receipt of the message. There is no reduction in uncertainty about the message.

    162. Comment by Zachriel — January 21, 2010 @ 11:23 am

  162. ID guy Says:
    January 21st, 2010 at 12:15 pm

    So if someone comes along who didn't have the knowledge of the first four digits then information suddenly springs forth from the once informationless sequence?

    Say you are transmitting a message to someone who already knew the information you were about to bestow.

    Did that transmission take place?

    Were any half-bits transmitted?

    If I take some nylonase, some mayonase and some bread would I be in a better or worse position to save the world from doom in 2012?

    163. Comment by ID guy — January 21, 2010 @ 12:15 pm

  163. Zachriel Says:
    January 21st, 2010 at 12:37 pm

    ID guy: Say you are transmitting a message to someone who already knew the information you were about to bestow.

    Don't confuse knowledge with information. It's not the semantic meaning, but the exact sequence of symbols. If only one possible message could be received, if the receiver knows exactly what each new symbol in the data-stream will be, then there is no Shannon Information.

    Shannon estimated the entropy of written English to be between 0.6 and 1.3 bits per character.

    Shannon, Prediction and Entropy of Printed English, Bell Systems Technical Journal 1951.

    164. Comment by Zachriel — January 21, 2010 @ 12:37 pm

  164. ID guy Says:
    January 21st, 2010 at 1:27 pm

    information:

    1 : the communication or reception of knowledge or intelligence
    2 a (1) : knowledge obtained from investigation, study, or instruction

    But I see you like to chop up what I say and respond to it out-of-context.

    Say you are transmitting a message to someone who already knew the information you were about to bestow.

    Did that transmission take place?

    Were any half-bits transmitted?

    If only one possible message could be received, if the receiver knows exactly what each new symbol in the data-stream will be, then there is no Shannon Information.

    So if you already have the knowledge of the incoming signal then when you receive the signal you will not have any new knowledge.

    That should go without saying.

    But say there is a professor giving a lecture.

    Half of the students know exactly what letters, symbols and words the professor will use in the exact sequence she will use them.

    The other students are ignorant- don't have such knowledge- ie information.

    Those students are given nylonase with mayonase sandwiches.

    The other students have pizza and beer.

    Do you see the problem?

    165. Comment by ID guy — January 21, 2010 @ 1:27 pm

  165. ID guy Says:
    January 21st, 2010 at 1:31 pm

    Zachriel:
    In our example, that means the first four digits have no information as we already know what they are *before* receipt of the message.

    Zachriel:
    Don't confuse knowledge with information.

    If we "already know what they are", your words, then that means we have knowledge of.

    IOW don't confuse Zachriel's bloviations with information.

    166. Comment by ID guy — January 21, 2010 @ 1:31 pm

  166. Zachriel Says:
    January 21st, 2010 at 1:38 pm

    ID guy: Say you are transmitting a message to someone who already knew the information you were about to bestow.

    As already pointed out, you are using the term "information" ambiguously. Shannon Information doesn't concern semantic knowledge, but only knowledge of a specific sequences of symbols. If you are transmitting on a noiseless channel to someone who already knows the exact sequence of symbols, then no Shannon Information is transmitted.

    The point of this entire subdiscussion has been that you insist that Shannon Information doesn't consider fractional bits when considering the ensemble of all possible messages. Even when it is pointed out to you that Shannon said, "a decimal digit is about 3 1/3 bits," it doesn't seem to faze you.

    Apparently, Shannon didn't understand Shannon Information.

    167. Comment by Zachriel — January 21, 2010 @ 1:38 pm

  167. ID guy Says:
    January 21st, 2010 at 1:44 pm

    Zachriel:
    As already pointed out, you are using the term "information" ambiguously.

    Nice projection.

    Shannon Information doesn't concern semantic knowledge,

    I know that. That is the reason Meyer says it pertains only to mere complexity. And as such useless in this debate.

    If you are transmitting on a noiseless channel to someone who already knows the exact sequence of symbols, then no Shannon Information is transmitted.

    Something is transmitted.

    What is it?

    The point of this entire subdiscussion has been that you insist that Shannon Information doesn't consider fractional bits when considering the ensemble of all possible messages.

    That is flat out false.

    I was only concerned with transmitting a fraction of a bit.

    So what we have is Zachriel misrepresenting what I said in order to make brownie points with the fairies.

    You must be very proud of yourself…

    168. Comment by ID guy — January 21, 2010 @ 1:44 pm

  168. ID guy Says:
    January 21st, 2010 at 1:47 pm

    ID Guy said::

    How does one transmit "about a half of bit"?

    I am pretty sure Shannon was concerned with the transmission and storage of bits.

    Did he discuss 1/2 bit transmission and storage?

    169. Comment by ID guy — January 21, 2010 @ 1:47 pm

  169. Zachriel Says:
    January 21st, 2010 at 3:00 pm

    Zachriel: If we assume a uniform distribution of amino acids, then there are about 4½ bits per amino acid.

    ID guy: How does one transmit "about a half of bit"?

    We've tried to explain that to you, but it's not clear you want to understand. However, it is clear that Shannon spoke in terms of partial bits of Information. Shannon Information is measured over an ensemble of possible messages. So a decimal digit is log2(10) bits as there are 10 possible messages of equal probability.

    A binary signal only conveys a bit of Shannon Information if the receiver can't guess (with better than random chance) the state of that signal. If the receiver can make a reasonable guess, then it conveys less than a bit of information. If the receiver knows what that signal will be with certainty, then it transmits zero information.

    Examples:

    "a decimal digit is about 3 1/3 bits."
    If we assume a uniform distribution of amino acids, then there are about 4½ bits per amino acid.
    Printed English, between 0.6 and 1.3 bits per character.

    The last example can be tested by allowing people to guess what letter is next in an English language text. That's what Shannon did.

    Of-en, th-r- -s lit-le unc-r-aint-.

    Shannon, Prediction and Entropy of Printed English, Bell Systems Technical Journal 1951.

    170. Comment by Zachriel — January 21, 2010 @ 3:00 pm

  170. ID guy Says:
    January 21st, 2010 at 3:26 pm

    Zachriel,

    You aren't even addressing the question.

    And I find that funny as hell…

    171. Comment by ID guy — January 21, 2010 @ 3:26 pm

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