Biological Information

  1. ‘Information’, ‘data’ and ‘media’ are distinct concepts. Media is the mechanical support for data and can be any material including DNA and RNA in biology. Data is the symbols that carry information and are stored and transmitted on the media. ACGT nucleotides forming strands of DNA are biologic data. Information is an entity that answers a question and is represented by data encoded on a particular media. Information is always created by an intelligent agent and used by the same or another intelligent agent. Interpreting the data to extract information requires a deciphering key such as a language. For example, proteins are made of amino acids selected based on a translation table (the deciphering key) from nucleotides.
  2. Information is entirely separate from matter. The same media (matter) may contain data representing information for one or more users, or random noise if the same bits of data have been randomly configured. Furthermore, without a deciphering key, one user’s information is random noise to another (like bird songs to unrelated birds). Information can be encoded in different ways (like distinct languages), resulting in unequal data sets. The size of the data is [in practice] always larger than the information carried due to redundancy which is necessary to maintain the integrity of the carried or stored information.
  3. The biologic cellular system is strikingly similar to human built autonomous information systems and unlike anything else observable in the inert universe. Media can be anything including any collection of atoms and, without a decoding key, the same media can support an infinity of data. For instance, a DNA chain encodes one set of data when read left to right, another when read in reverse, yet another when read pair-by-pair, and so on. But in living organisms, DNA actually encodes specific information that is uniquely decoded with a key. Furthermore, the information in the DNA is also redundantly encoded to ensure its long term integrity. Aside from DNA and RNA, we can observe many other information systems in nature (with decoding keys such as pheromones, antigens, and hormones), but all are limited to the living.
  4. DNA mutations are wrongfully interpreted by some as spontaneous information generation, however the DNA limitations show that DNA is not ‘the code of life’, but only a configurable portion of ‘the code of life’. In addition, the adaptive mutations appear limited in range, reversible when the stimulus is removed, and repeatable, indicating their non-random character (as in “the peppered moth”, “Darwin’s finches”, and antibiotic resistance). This is exactly how advanced human designed computer systems behave – they have been built with adaptability in mind, therefore to the untrained eye these systems seem completely autonomous and infinitely auto-reconfigurable (”Artificial Intelligence” fallacy).
  5. Information cannot just pop into existence in the absence of an intelligent agent. That is why all noise-based information generating attempts including all “infinite monkey” experiments have failed and that is why “Artificial Intelligence” will never “rise”. Separating information from noise has been a very important human activity for thousands of years and success in this endeavor has always been based on two critical elements: deciphering key and redundant encoding.
  6. Information can exist for a long time without an intelligent agent. Information can be stored, transmitted and downloaded into machines that perform certain operations regardless of whether the intelligent agent is still around or not. Based on all our knowledge about information, not observing the intelligent agent at work should never lead to the absurd assumption that the information machine “arose without a designer”. It is no coincidence that teleological terms such as “function” and “design” appear frequently in the biological sciences.
  7. Data is everywhere (including fossil record and marks of past events such as asteroid impacts), but that data becomes information only to intelligent agents like us (organisms) and only when we learn to interpret it and to make predictions (answer questions). When we look at the sedimentation and erosion, we take that data and make information from it based on our knowledge. There is no information in the rocks, just data.

Summary:

  1. ‘Information’, ‘data’ and ‘media’ are distinct concepts
  2. Information is entirely separate from matter
  3. Biologic cellular systems are strikingly similar to human built autonomous information systems and unlike anything else observable in the inert universe
  4. DNA mutations are wrongfully interpreted by some as spontaneous information generation
  5. Information cannot just pop into existence in the absence of an intelligent agent
  6. Information can exist for a long time without an intelligent agent
  7. Data is everywhere (including fossil record), but that data becomes information only to intelligent agents

Links:

https://schneider.ncifcrf.gov/

https://plato.stanford.edu/entries/information-biological/

https://evolutionnews.org/2014/08/biological_info_1/

http://www.worldscientific.com/worldscibooks/10.1142/8818#t=toc

https://discourse.biologos.org/t/information-entropy/35327/21

https://uncommondescent.com/intelligent-design/genetic-novelty-conference-errors-cannot-explain-genetic-novelty-and-complexity/#comment-651105

Notes:

Con: Information is just entropy.

Pro: Shannon never said “Information = Entropy”. Wikipedia quote: “Entropy is a measure of unpredictability of the state, or equivalently, of its average information content. Hence Entropy is just an attribute of Information. In addition, information always requires a deciphering key and some redundancy, both of which reduce entropy. Information is meaningful only to the sender and receiver (and the spy). To all others it’s noise.

Con: Random number generators can open any lock.

Pro: The human opens the lock, not the random generator. The random generator is just a tool to the human.

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351 thoughts on “Biological Information

  1. Rumraket: It can be treated as if it was a string of symbols.

    If it’s not literally a string of symbols then Shallit’s questions are nonsense.

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  2. Mung: If it’s not literally a string of symbols then Shallit’s questionsare nonsense.

    Explain why.

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  3. Rumraket: Then define information.

    what is conveyed or represented by a particular arrangement or sequence of things.

    (in information theory) a mathematical quantity expressing the probability of occurrence of a particular sequence of symbols, impulses, etc., as contrasted with that of alternative sequences.

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  4. Rumraket: Explain why.

    Because his version of information requires literal symbols. Didn’t you read what I quoted earlier?

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  5. Mung: what is conveyed or represented by a particular arrangement or sequence of things.

    Then tree rings contain information. LOL.

    (in information theory) a mathematical quantity expressing the probability of occurrence of a particular sequence of symbols, impulses, etc., as contrasted with that of alternative sequences.

    Then evolution can increase information by mutation, as mutation can increase or decrease the probability of occurence of a particular sequence of symbols.

    Thanks or playing.

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  6. Mung: Because his version of information requires literal symbols. Didn’t you read what I quoted earlier?

    No it doesn’t, nowhere does it say it requires literal symbols. What did you quote that contradicts this?

    In fact, your dictionary copy-paste only suggests symbols as one among several other possibilities: “(in information theory) a mathematical quantity expressing the probability of occurrence of a particular sequence of symbols, impulses, etc., as contrasted with that of alternative sequences.”

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  7. Mung: Because his version of information requires literal symbols. Didn’t you read what I quoted earlier?

    Let me see …

    Mung: (in information theory) a mathematical quantity expressing the probability of occurrence of a particular sequence of symbols, impulses, etc., as contrasted with that of alternative sequences.

    Who knew? I looks a lot like the definition quoted by Mung includes things other than literal symbols. I’d advice you to take a course in reading comprehension Mung

    ETA: Almost Nija’d!

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  8. Mung: what is conveyed or represented by a particular arrangement or sequence of things.

    By that definition tree rings contain information.

    IDiots sure love to equivocate with their definitions, don’t they? 🙂

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  9. Mung,

    what is conveyed or represented by a particular arrangement or sequence of things.

    In this case the tree rings do not contain information as they need to be decoded to understand what they “convey or represent”.

    Is decoding required to calculate probability?

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  10. colewd: In this case the tree rings do not contain information as they need to be decoded to understand what they “convey or represent”.

    If tree rings need to be decoded then it is the environment which creates the code. So is the environment creating the information we decode?

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  11. newton,

    If tree rings need to be decoded then it is the environment which creates the code.

    Can you expand on this? I am not following your logic.

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  12. colewd:
    newton,

    Can you expand on this? I am not following your logic.

    There are many examples similar to tree ring patterns that give information about past climate. Snow cores, lake varves and so on. Paleo-climatology. Is the information gleaned initially stored by environmental fluctuations? I’d say so.

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  13. Alan Fox,

    Is the information gleaned initially stored by environmental fluctuations? I’d say so.

    Do you mean the pattern is caused by environmental fluctuations?

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  14. colewd: In this case the tree rings do not contain information as they need to be decoded to understand what they “convey or represent”.

    Then me sending you an encoded message, like morse-code, does not convey information. Which is obviously ridiculous.

    By the same token, the genetic code that specifies the amino acid sequence of proteins, from the nucleotide sequences of RNA and DNA, does not transfer information when it is translated.

    Okay, okay Bill, I’m fine with saying that (actually I’m not, it’s a ridiculous conclusion). But then protein-coding DNA does not contain information, thus the evolution of new protein coding genes is not required to create any new information.

    It is obvious that you are just flailing around trying to come up with some sort of claim that prevents something other than a designer from having created information, but it keeps coming back to bite you. Just give up. Evolution, and many other blind physical processes, can create information. Get over it, move on, find some other reason to believe what you believe.

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  15. Rumraket,

    Then me sending you an encoded message, like morse-code, does not convey information. Which is obviously ridiculous.

    If I have the ability to translate the code then it is information. Without translation it is data. I can have a computer translate the code for me but we know the translation key or mechanism required a designed artifact.

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  16. colewd:
    Rumraket,

    If I have the ability to translate the code then it is information.

    Then tree rings are information because you can translate them.

    Without translation it is data.

    So the same thing can go back and forth just by someone looking at it? In fact, just by something interacting with it?

    I can have a computer translate the code for me but we know the translation key or mechanism required a designed artifact.

    We don’t know that. I don’t see how a designed artifact is required to translate DNA or RNA sequence into amino acid sequence, nor do I know what designed artifact is required to translate tree rings into the age of the tree, or knowledge of past climates where the tree lived.

    You’re just making shit up as you go along.

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  17. Rumraket,

    We don’t know that.

    I think we do. Can you translate Morris code without human knowledge as a filter or a designed artifact to translate it? Can you translate rings on a tree without human knowledge or a designed artifact that can translate the rings into information?

    If the answer is no then the inference that the living mechanism of transcription, splicing, translation is designed is reasonable.

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  18. colewd: I think we do. Can you translate Morris code without human knowledge as a filter or a designed artifact to translate it?

    Why does it matter what I can personally accomplish? We are talking about whether tree rings contain information, not about who or what is capable of extracting that information.

    Can you translate rings on a tree without human knowledge or a designed artifact that can translate the rings into information?

    That has nothing to do with whether tree rings contain information or how it got there. Even if I could not do that, that would still not mean tree rings did not contain information. Nor would it mean tree rings had to be designed in order for information to be contained in their structure, number, and order.

    You seem to be saying that in so far as there is no one around who is capable of extracting the information, then there IS no information. That it only becomes information when looked at. Again, if that is so, then DNA isn’t information as no designed artifact or intelligence is required for it’s translation into proteins.

    By insisting that the translation system is designed, you are merely begging the question.

    If the answer is no then the inference that the living mechanism of transcription, splicing, translation is designed is reasonable.

    None of your assertions follow from each other. You are just making shit up by piling more and more unsupported claims on top of each other.

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  19. I’m afraid I find the discussion on the definition of information somewhat beside the point. What I cannot understand is the biological origin of the translation system, which is required to allow for a linkage between genotype and phenotype, and thus is an essential part of the evolutionary mechanism. (since natural selection acts on the phenotype, but variation occurs in genotypes). So the question is how can something required for evolution (translation), evolve.

    Possible answers include alternative kinds of evolution, but I havent seen these described. If anyone can cite something I would love to see it. (Ribozymes dont count, I know the work of Joyce, Koonin and Szostack groups already).

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  20. Sy Garte:
    I’m afraid I find the discussion on the definition of information somewhat beside the point. What I cannot understand is the biological origin of the translation system, which is required to allow for a linkage between genotype and phenotype, and thus is an essential part of the evolutionary mechanism. (since natural selection acts on the phenotype, but variation occurs in genotypes). So the question is how can something required for evolution (translation), evolve.

    Possible answers include alternative kinds of evolution, but I havent seen these described. If anyone can cite something I would love to see it. (Ribozymes dont count, I know the work of Joyce, Koonin and Szostack groups already).

    We don’t know the origin of the translation system. Hypotheses have been suggested, such as Wolf & Koonin 2007 (Biol Direct. 2007 May 31;2:14.), but that is what they are at this stage, untested hypotheses. There are still many things we don’t understand about the origin of life. We don’t even know at what stage in the origin process that biological membranes came to have a role, whether they were there from the very beginning or later evolved in some sort of metabolism enclosed in another entity. These are all unknowns. Even if we were to find out how it could have happened, we still wouldn’t technically know that that is how it did happen.

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  21. Rumraket,
    Rum

    By insisting that the translation system is designed, you are merely begging the question.

    BC

    the inference that the living mechanism of transcription, splicing, translation is designed is reasonable.

    If I was insisting then yes I would be begging the question. If I am inferring based on other translation systems being from human intelligence or a designed artifact then I am not begging the question but making an inference from observation.

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  22. Rumraket,

    There are still many things we don’t understand about the origin of life.

    How about the origin of the eukaryotic cell?

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  23. colewd:
    Rumraket,

    How about the origin of the eukaryotic cell?

    We know a lot more about that, as there are many aspects of this event for which phylogenetic analysis can be brought to bear to shed light on it. That doesn’t mean we know everything about it, far from it, and it is still a difficult problem in the sense that many pieces of the picture is missing.

    But we are not in a similar state of near-total ignorance as we are for the origin of life.

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  24. colewd:
    Rumraket,
    Rum

    BC

    If I was insisting then yes I would be begging the question.If I am inferring based on other translation systems being from human intelligence or a designed artifact then I am not begging the question but making an inference from observation.

    Bill you didn’t make an inference, you made an assertion An inference is essentially an argument that has premises and a conclusion.

    What you did was merely to declare that if I can’t tell you how the information in tree rings (for example) can be “translated” into knowledge without intelligence, then that makes the conclusion that the translation system was designed, reasonable. But what is missing here is the actual act of inferential reasoning that connects the premise [I can’t tell you how the information in tree rings can be “translated” into human knowledge without intelligence] to the conclusion [the belief that the translation system of the genetic code was designed is plausible]. You are missing the key step of an inference: The actual inference. Nothing you’ve stated has increased the plausibility of the conclusion. In fact your “inference” is a textbook example of the argument from ignorance fallacy. The foundational premise is my ignorance, with which you seek to establish that a particular conclusion is plausible. That is patently invalid logic.

    And in any case, it is still completely irrelevant wrt to the claim advanced in the OP, which is that information can’t be created by evolution. Even IF the translation system was designed, and even IF translation systems REQUIRE design to originate, it would STILL not follow that an evolutionary process can’t create translatable biological information by mutation, drift, and selection.

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  25. Rumraket,

    .If I am inferring based on other translation systems being from human intelligence or a designed artifact then I am not begging the question but making an inference from observation.

    The observation is that all other systems that can translate are designed. The inference from the observation is that the transcription, splicing and translation system is designed.

    Nothing you’ve stated has increased the plausibility of the conclusion.

    Why not? As we show additional evidence that this type of mechanism is designed then the plausibility that this mechanism is designed is increased. If you found a translation mechanism in nature outside living organisms that could turn data into information then the plausibility would go down.

    And in any case, it is still completely irrelevant wrt to the claim advanced in the OP, which is that information can’t be created by evolution. Even IF the translation system was designed, and even IF translation systems REQUIRE design to originate, it would STILL not follow that an evolutionary process can’t create translatable biological information by mutation, drift, and selection.

    I think this is a valid point however the case whether evolution can create biological information is still open in my mind. As a minimum any random change has a much greater chance of losing information then gaining it.

    Joe’s argument of gaining information by a single AA substitution is logical but unless there is a sustainable mechanism the claim is of little consequence.

    From this perspective the origin of the eukaryotic cell which includes
    -the origin of a eukaryotic ribosome
    -the origin of a cell nucleus
    -the origin of ubiquitin system
    -the origin of the splicosome
    -the origin of chromatin structure
    -the origin of the nuclear pore complex

    Clearly rivals OOL from the quantity of novel genetic information that needs to be explained along with the origin of a novel transcription and translation system and cellular control system that is completely different and substantially more complex then what we find in prokaryotic cells.

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  26. colewd: How about the origin of the eukaryotic cell?

    How about the origin of the designer of the eukaryotic cell?

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  27. Rumraket: Even IF the translation system was designed, and even IF translation systems REQUIRE design to originate, it would STILL not follow that an evolutionary process can’t create translatable biological information by mutation, drift, and selection.

    I think this is an important statement because it very effectively separates the two unrelated issues of 1. the origin of life (and the origin of biological evolution, LUCA, etc) from the question of 2. evolutionary mechanisms. Any discussion or argument that does not make this critical distinction between these entirely separate phenomena is, I believe, ultimately doomed to fail.

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  28. colewd:
    If I am inferring based on other translation systems being from human intelligence or a designed artifact then I am not begging the question but making an inference from observation.

    No Bill, this is more like an equivocation. We call the mRNA-to-Protein process “translation” by metaphor. However, it’s not at all like a human-made translation system. Concluding from metaphorical descriptions would qualify as equivocation, not as inference.

    colewd:
    The observation is that all other systems that can translate are designed. The inference from the observation is that the transcription, splicing and translation system is designed.

    But you’re forgetting that “transcription,” “splicing” and “translation” happen everywhere on their own within life forms, while human-made systems are made by a life form that depends, deeply, on those systems. You’re therefore putting the cart before the horse. Also, again, the names we’ve given to those systems are given by metaphor for the obvious reason that we’re humans. Again, equivocation.

    colewd:
    Why not? As we show additional evidence that this type of mechanism is designed

    I think you’re chanting victory too soon. You haven’t shown any evidence that these mechanisms are designed, you’ve only shown that you can be fooled by metaphors, despite the cart-before-the-horse problem that you’d rather not contemplate.

    colewd:
    then the plausibility that this mechanism is designed is increased.If you found a translation mechanism in nature outside living organisms that could turn data into information then the plausibility would go down.

    Why outside of living organisms? You’re very happy to use a single living system to make your “inference.” So, asking us to reach beyond living organisms for an answer, when you’re cherry-picking from one for your “inference,” seems like quite the double standard to me. I’d say that the mere fact that life forms do all of that without the interference of any designers makes the designer “inference” even more problematic. If it works on its own, without any designers intervening, then the probability that it originated without designer intervention gets quite a load of points. I’d say p=1.00.

    colewd:
    I think this is a valid point however the case whether evolution can create biological information is still open in my mind.As a minimum any random change has a much greater chance of losing information then gaining it.

    Which is why we observe such an amount of evidence for purifying selection. That pretty much shows that evolution is the only game in town.

    colewd:
    Joe’s argument of gaining information by a single AA substitution is logical but unless there is a sustainable mechanism the claim is of little consequence.

    Joe presents a sustainable mechanism. Sustainability only depends on the systems being out of equilibrium, which is what the energy flow provides.

    colewd:
    From this perspective the origin of the eukaryotic cell which includes
    -the origin of a eukaryotic ribosome
    -the origin of a cell nucleus
    -the origin of ubiquitin system
    -the origin of the splicosome
    -the origin of chromatin structure
    -the origin of the nuclear pore complex

    There’s data for some of that, and I see more data coming from the sequencing of prokaryotes previously unknown for us. Much might remain obscure, but I doubt that you’d like to make your already problematic “inference” into merely a god-of-the-gaps argument.

    colewd:
    Clearly rivals OOL from the quantity of novel genetic information that needs to be explained along with the origin of a novel transcription and translation system and cellular control system that is completely different and substantially more complex then what we find in prokaryotic cells.

    Well, for one, no, they’re not “completely different” from what we find in prokaryotic cells. The claim is false even though we’re still discovering prokaryotes.

    Previously I complained a similar claim of yours as being a problem of focusing on humans and comparing them to a few other organisms. I added that to know if there’s increases in information, rather than redistribution, you’d have to know of all the life forms living at the time.

    Let me try and explain why I said that. When the first eukaryotes originated, there was loads and loads of other life forms, only not eukaryotic. So, the origin of the “information” in eukaryotic cells might be just the coming together of systems developed across prokaryotes, thus being “new” information in terms of getting together, but mostly a redistribution of information, since the systems existed previously.

    For example, if you look for articles on the ubiquitin system and prokaryotes, you might find that some gene sets, homologs to those in the ubiquitin system, have been found next to each other in prokaryotic organisms recently sequenced. If those results have really uncovered the descendants of an ancient prokaryotic ubiquitin system (yes, I’m been careful because, even though this aligns with what I think, the results are somewhat recent), then the scientists who are now looking for more organisms of this newly discovered group of organisms might be able to develop good hypotheses, and perhaps a full theory, on the origins of the ubiquitin system.

    Just like that, other systems might come from functional groups of genes originating in other prokaryotes. After all, the first eukaryotes were very prokaryotic, and thus, the rearrangement of systems into some newly evolved cells is not that much of a stretch.

    I hope you’ll read this carefully. If anything is unclear, let me know. I’m always for improving my explanations.

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  29. Entropy,

    If it works on its own, without any designers intervening, then the probability that it originated without designer intervention gets quite a load of points. I’d say p=1.00.

    If your car works without design intervention does that mean it originated without a designer?

    No Bill, this is more like an equivocation. We call the mRNA-to-Protein process “translation” by metaphor. However, it’s not at all like a human-made translation system. Concluding from metaphorical descriptions would qualify as equivocation, not as inference.

    It’s not equivocation and it’s not a metaphor. It is 3 nucleic molecules translating to 1 of 20 AA molecules. Computers are 8 bits translating to 256 ascii bits.

    Joe presents a sustainable mechanism. Sustainability only depends on the systems being out of equilibrium, which is what the energy flow provides.

    Energy flow and genetic data are separate things. I understand you think energy can generate data on its own. I have no idea why you would think this. I look forward to learning Joe’s theory.

    Let me try and explain why I said that. When the first eukaryotes originated, there was loads and loads of other life forms, only not eukaryotic. So, the origin of the “information” in eukaryotic cells might be just the coming together of systems developed across prokaryotes, thus being “new” information in terms of getting together, but mostly a redistribution of information, since the systems existed previously.

    How do you explain information coming together? The eukaryotic cell has tens of millions of nucleotides that prokaryotic cells don’t and a boat load of additional functions.

    How do you explain all this data coming together in anticipation of multicellular life without a plan?

    Well, for one, no, they’re not “completely different” from what we find in prokaryotic cells. The claim is false even though we’re still discovering prokaryotes.

    They are very different as eukaryotic cells are capable of supporting multicellular organisms. We may be struggling with what “very different” means. Prokaryotic cells don’t have.
    A nucleus
    A nuclear pore complex
    A spliceosome
    A chromosome structure
    A ubiquitin system
    A golgi apparatus
    Mitochondria
    etc.

    Just like that, other systems might come from functional groups of genes originating in other prokaryotes. After all, the first eukaryotes were very prokaryotic, and thus, the rearrangement of systems into some newly evolved cells is not that much of a stretch.

    Do you have any real evidence or is this based on your “it has to have started simpler” hypothesis?

    I hope you’ll read this carefully. If anything is unclear, let me know. I’m always for improving my explanations.

    What is unclear to me is your objection to design based on designers requiring the same components that are claimed to be designed.

    This appears arbitrary to me and not based on sound reasoning unless you are trying to push philosophical atheism as an a priori assumption. I am coming from the view that reality may exist outside our space-time.

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  30. colewd: What is unclear to me is your objection to design based on designers requiring the same components that are claimed to be designed.

    This appears arbitrary to me and not based on sound reasoning unless you are trying to push philosophical atheism as an a priori assumption

    What does atheism have to do with this, Billy? Are you saying that ID is in fact about the designer’s identity (God)?

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  31. colewd:
    If your car works without design intervention does that mean it originated without a designer?

    Cars don’t reproduce. We can find many things around cars that make it evident they were designed, etc.

    For the case I was making, we’re talking about something we find everywhere, and where no designer intervention is anywhere to be seen. No plans, no tools, no prototypes, no evidence of some beings coming every once in a while to trick life forms, how they did what they did, etc.

    But that’s not the way to approach scientific problems (by denying a foolish “hypothesis” such as design). We have to start with what we have. What we have is things that reproduce and work and do lots of stuff on their own. So, we have to start by analyzing what we do have, the life forms themselves. While doing that, scientists have discovered that, just the way things work, it looks a lot like life forms diverge. That gives us a clue about evolution. Then we have many more lines of evidence, and all of it leads to lots (if not universal) of common descent, and evolutionary phenomena explain things all right. So, trying to fit things into “it must have been designed,” looks like unscientific desperate attempts at religious apologetics based on poor philosophy, lack of understanding about the little but important knowledge we’ve already gathered about how nature works, while cherry-picking facts and factoids and making fools out of themselves by numerical smoke-and-mirrors, based on the very same failed foundations of any other apologetics.

    colewd:
    It’s not equivocation and it’s not a metaphor.It is 3 nucleic molecules translating to 1 of 20 AA molecules.Computers are 8 bits translating to 256 ascii bits.

    Whether you want to admit to it or not, it’s still both equivocation and metaphors.

    colewd:
    Energy flow and genetic data are separate things.

    Sure. But I double dare you to find me a single instance where energy flow and data generation, of any kind, are unlinked.

    colewd:
    I understand you think energy can generate data on its own.

    Not on its own, it’s an interplay between some random phenomena, which makes the out-of-equilibrium thing in both energy terms, and matter terms. The interplay between energy flow, natural “laws,” and matter is what generates all of that interesting stuff.

    colewd:
    I have no idea why you would think this. I look forward to learning Joe’s theory.

    It’s hard work Bill. I find it hard to explain myself. But the fact is that the out-of-equilibrium dynamics is what’s behind the whole thing, big time. We would not be able to design anything without it ourselves. That points right to the cart-before-the-horse problem from another angle.

    colewd:
    How do you explain information coming together?

    Horizontal gene transfer, endosymbiosis, evolutionary processes.

    colewd:
    The eukaryotic cell has tens of millions of nucleotides that prokaryotic cells don’t and a boat load of additional functions.

    Did you read what I wrote? It seems like scientists discovered most-if-not-all of the components of the ubiquitin system in some prokaryotes. I’d expect that by the time eukaryotes started their evolution, many of those systems you claim to exist only in eukaryotes had some precursors in prokaryotes. I think that there’s little innovation since the planet became life-rich. So, even if there was no trace of the original systems today, there’s nothing outrageous about the idea that precursor systems existed by those original times.

    You seem rather skeptical about what’s available in nature, despite nature being the most reasonable source of everything we see. At the same time you’re not too judgemental about ID, which is irrational to the point of pain. The difference between you and me is that I don’t see any reason to depart from rational investigation, while you think that numerology-smoke-and-nirrors should convince everybody. As I said, maybe there’s many things we will be unable to trace to their origins. That won’;t make me any more inclined to accept something as fallacious as ID.

    colewd:
    How do you explain all this data coming together in anticipation of multicellular life without a plan?

    Why would I think of it happening in anticipation to anything? That would be begging the question (on your part). I just think of it as “tension.” With the abundance of life, there would be a lot of potential avenues for evolutionary paths, which made it possible for “something else” to happen at one point or another, and here we are.

    colewd:
    They are very different as eukaryotic cells are capable of supporting multicellular organisms.We may be struggling with what “very different” means.Prokaryotic cells don’t have.
    A nucleus
    A nuclear pore complex
    A spliceosome
    A chromosome structure
    A ubiquitin system
    A golgi apparatus
    Mitochondria
    etc.

    I just explained to you that some of them do have an ubiquitin system, yet you repeat that one in your list? How far do you think we’ll go if you don’t take even the one that already seems to be there? (Besides prior prokaryotic ubiquitin-like proteins discovered years ago.)

    Mitochondria are pretty much prokaryotes, so I think you’re listing it for rhetorical effect.

    So, again, maybe there will be more discoveries leading to the rest. Yet. I insist, even if the evidence was gone by the eons since the original eukaryotes, we’d be left with a gap in knowledge, not with evidence of design. You understand the difference, don’t you?

    colewd:
    Do you have any real evidence or is this based on your “it has to have started simpler” hypothesis?

    I didn’t say anything about starting simple. If life forms were abundant when eukaryotes arose, that fact alone means there was already a lot of complexity.

    colewd:
    What is unclear to me is your objection to design based on designers requiring the same components that are claimed to be designed.

    Why would this be unclear? It’s obvious that if designers are complex organisms themselves, trying to explain them as the result of design doesn’t solve anything. We’d be left with the very same question: how did the complexity of any designer arise? We’d be left with talking about how natural phenomena work, and how could it lead to the first designers anyway. So why do something that foolish, when there’s no evidence of prior designers in the first place? Why not try and get the right answers now, instead of leaving them for things we cannot even demonstrate to have existed (those previous designers), and we’d not have any access to for analyses?

    colewd:
    This appears arbitrary to me and not based on sound reasoning unless you are trying to push philosophical atheism as an a priori assumption.I am coming from the view that reality may exist outside our space-time.

    See what I say? ID is purely religious in nature. Otherwise you’d see why I prefer to be lead by the data, rather than by some a priory commitment to the gods.

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  32. colewd: Joe’s argument of gaining information by a single AA substitution is logical but unless there is a sustainable mechanism the claim is of little consequence.

    I was going to respond to colewd’s question earlier, with a couple of paragraphs on why energy is needed for the reproduction of evolving systems, and how change of the distribution of genotypes (in my model owing to their different rates of loss of energy) constituted information in both the Shannon and the Orgel/Szostak functional information sense. But I see that the argument has been made to colewd by others here.

    And that colewd falls back on the moldy old argument that yes, we can explain how some information gets into the genome but we can’t explain how a really-really-lot of really-really-important information gets there. In other words, the moldy old macro-micro argument, but this time informationized.

    (By the way, I try to use the phrase that information “gets into” the genome so as to avoid the endless arguments about whether it is new information or was somehow lying around out there before).

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  33. dazz,

    What does atheism have to do with this, Billy? Are you saying that ID is in fact about the designer’s identity (God)?

    ID has a lot of sides to it and certainly one of them is support of the existence of God.

    ID as an academic study is about detecting design in nature. If you set an academic rule that you cannot discuss design in nature because we have no direct evidence of a designer then this appears to be an arbitrary philosophical objection.

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  34. Entropy,

    See what I say? ID is purely religious in nature. Otherwise you’d see why I prefer to be lead by the data, rather than by some a priory commitment to the gods.

    I think ID has religious implications yet it also has value to science.

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  35. colewd:
    dazz,

    ID has a lot of sides to it and certainly one of them is support of the existence of God.

    ID as an academic study is about detecting design in nature.If you set an academic rule that you cannot discuss design in nature because we have no direct evidence of a designer then this appears to be an arbitrary philosophical objection.

    Bullshit. Pure, unadulterated and dishonest creotard bullshit.
    (Lots of redundant terms there, I know)

    It’s IDiots who constantly claim that ID is not about who the designer is. But if you think it is, it’s up to you to show evidence, yes, empirical evidence of the existence of your God.

    Of course there’s a philosophical commitment in science, it wouldn’t be science if there wasn’t. Is your God a valid scientific explanation that can be empirically tested? No? Too bad buddy, that’s YOUR problem, not science’s

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  36. Joe Felsenstein,

    And that colewd falls back on the moldy old argument that yes, we can explain how some information gets into the genome but we can’t explain how a really-really-lot of really-really-important information gets there. In other words, the moldy old macro-micro argument, but this time informationized.

    There was a reason someone came up with that moldy old argument:-)

    The information in the genome is organized in a sequence. Through serendipity you can get an adaption through random change but eventually the laws of statistics result in loss of that information. This is John and Bill’s argument and I have not seen a reasonable challenge yet.

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  37. dazz,

    It’s IDiots who constantly claim that ID is not about who the designer is. But if you think it is, it’s up to you to show evidence, yes, empirical evidence of the existence of your God.

    Why is ID such a problem for you? It is just an academic argument. Sure it supports the existence of God but so what?

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  38. colewd:
    dazz,

    Why is ID such a problem for you?It is just an academic argument.Sure it supports the existence of God but so what?

    Because I have a lot of respect for science, and none for pathetic apologists who shit all over it while pretending they’re doing science.

    And no, it’s not an “academic” argument, and no, it doesn’t support the existence of God, scientifically or otherwise

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  39. dazz,

    . Is your God a valid scientific explanation that can be empirically tested?

    No. ID is an argument for design in nature based on “inference to the best explanation”. God would be a second level inference based on the evidence pointing to design.

    The great irony here is that Darwin’s theory was based on making “inference to the best explanation” a valid scientific argument.

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  40. colewd:
    dazz,

    No.ID is an argument for design in nature based on “inference to the best explanation”.God would be a second level inference based on the evidence pointing to design.

    The great irony here is that Darwin’s theory was based on making “inference to the best explanation” a valid scientific argument.

    And we’ve been telling your for ages that “design” is not a scientific explanation at all, let alone the best, but you’re too fucking stupid to understand.

    There’s no irony anywhere, Darwin’s was a proper explanation that stood the test of time and evidence.

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  41. dazz,

    Because I have a lot of respect for science, and none for pathetic apologists who shit all over it while pretending they’re doing science.

    Are you really this naive?

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  42. Alan Fox: There are many examples similar to tree ring patterns that give information about past climate.

    Didn’t you read the OP?

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  43. colewd: Is decoding required to calculate probability?

    No.

    If you have a source transmitting a sequence of zeros and ones you don’t need to decode what the sequences mean and the sequences don’t even have to have any meaning at all to them, they could be generated randomly.

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  44. colewd:
    dazz,

    Are you really this naive?

    Get back to me when an IDiot has explained a single thing about anything. Until then: derp

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  45. Mung,

    If you have a source transmitting a sequence of zeros and ones you don’t need to decode what the sequences mean and the sequences don’t even have to have any meaning at all to them, they could be generated randomly.

    If you had a string of 80 characters how would you calculate the probability that they are the result of random character generation?

    If you were able to show that they were 10, 8 bit ascii characters then you could do a probability calculation. This example requires decoding.

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