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. Mung,
    Yes, I do.
    Would you like to have a go at explaining to us what you think they are talking about?

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  2. I believe I understand what they are talking about too. And that it has terrible implications for creationist claims about the ability of evolution to create information.

    I completely fail to see how those references establish that none of us have any idea what we’re talking about. I’d like for Mung to explain why he thinks that.

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  3. Mung:

    Let Σ be an alphabet and let Σ∗ be the corresponding free monoid. Fix a finite subset U of Σ∗, where each sequence has finite length, and a measurable function F, where the measure is defined over U. U is referred to as sequence space (with respect to function F). Let Nk be the number of sequences in U that has a value
    of the measure at least k. Then, FI(k) = − log2(Nk/|U|)

    How come they don’t use the entire sequence space Σ∗ for their calculations like IDiots do?

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  4. PeterP: Human oocytes are arrested in meiosis during fetal development so no DNA repair happening at that front. It isn’t uncommon, in my experience, that the conversation on mutations often flip, without regard to distinction, between germline and somatic cells despite their obvious differences and lifestage ramifications.

    Point taken. I should have phrased that a little more carefully.

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  5. colewd: Me: I wouldn’t. DNA repair deals with damage before it ends up in the germline. Natural selection needs genetic variation to be expressed.

    Are you assuming that DNA repair does not exist in the germline?

    Can you put a little more thought into this?

    DNA repair deals with problems with the integrity of DNA molecules. We are talking about stuff like base pair mismatches, pyrimidine dimers and other structural distortions. These prevent the DNA from being properly transcribed and replicated and need to be repaired. But, and this is the important bit, DNA repair will never restore a deleterious allele to its wildtype counterpart. The reason is that deleterious alleles are being encoded by a structurally sound double-helical DNA molecule, so they are not recognised as anomalous by the DNA repair system.

    The removal of deleterious alleles by purifying selection is very different from this, as it is proceeds by selective elimination of unfit individuals! In normal English; organisms carrying deleterious alleles tend to leave fewer offspring. This simply is the process of natural selection as described by good ol’ C. Darwin, with the minor twist that the favorable variant is not some shiny new adaptation, but the established variant.

    I hope you can see now DNA repair and purifying selection are very different things.

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  6. colewd: Sure. I am thinking about the relationship between fitness and function where one can describe something very specific and the other is a description of something more general.

    Can we describe biological fitness as a measurement of the output (if you can) of a large set of interdependent biological functions?

    For the sake of argument at this point can we limit a biological function to an individual protein coding gene as that would merge with gpuccio’s definition of function?

    This is excellent, thanks. Yes, it is possible to decompose fitness into the molecular functions of individual biomolecules. The question I was specifically asking is how a particular molecular function would be preserved independently of purifying selection. In my view, conservation of functional information only occurs if that function is somehow correlated with survival and reproduction, i.e. biological fitness. A function that does not contribute to fitness is not conserved by purifying selection so needs to be actively maintained by the Designer. That is why I put in the joke of the Designer doing periodical check-ups 🙂

    Do you believe this to be true? Are there molecular functions in eukaryotes that are not being conserved by purifying selection (because they do not affect fitness), but are being actively maintained by some other unknown process? If so, what are those functions and what purpose do they serve?

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  7. Mung: colewd: When he learns to spout evolutionist bullshit he will be the star of the show.

    He’s an expert at that too.

    Saw what you did there 😉

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  8. Rumraket: That article argues why Shannon information is a poor use for determing functional information content. Because it argues that we need to consider the functionality of the information. That it is essentially only information if it is involved in some biological function.

    I would actually agree with that. But nowhere in that article is it shown that evolution can’t produce new functional information. Just that Shannon’s theory of information is a poor theory for doing that.

    Agreed. But did I understand correctly that these measures of functional information are based on Shannon information, with the added requirement that a string has to be capable of fulfilling some prespecified biological function?

    That would make a lot of sense to me, as natural selection would then add enormous amounts of functional (=fitness) information by enriching a population with genotypes of high fitness.

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  9. colewd: Are you assuming that DNA repair does not exist in the germline?

    Can you put a little more thought into this?

    DNA repair is also in operation in the germline, yes. But it isn’t perfect, mutations still slip through.

    Those mutations that still slip through, affect phenotypes for the better or worse (higher or lower fitness). Worse mutations cause lower fitness, so will automatically be selected against as carriers either die or have fewer offspring on average compared to non-carriers. That’s purifying selection in operation, killing off deleterious mutants.

    Purifying selection implies that something is at or near a local peak in the fitness landscape, so new mutants are almost always deleterious and thus get purged. Positive selection is when something is being driven up the slope towards the peak, from a lower position as a new mutant that has occurred is beneficial against an established allele with lower fitness. Then the mutation is said to be selected for as it rises in frequency in the population. The whole population is slowly moving up hill under positive selection.

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  10. DNA_Jock: Would you like to have a go at explaining to us what you think they are talking about?

    “They” was a reference to the people posting here, not to the papers I quoted. I should have made that more clear.

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  11. Rumraket: Amount. Quantity. How much information there is. Like “caloric content” of some food. It has so many joules pr. gram.

    I’d like to see a similar thing done for functional DNA, like a protein coding gene of some length. How much functional information is that? I’m assuming we measure it in bits.

    But they are not the same. “Caloric content” refers to something physical. There is something in the food that can be converted by physical means into something else. Don’t you agree? How is that true of “information content”?

    In order to answer this question, it helps to define a calorie. A calorie is a unit that is used to measure energy. The Calorie you see on a food package is actually a kilocalorie, or 1,000 calories. A Calorie (kcal) is the amount of energy needed to raise the temperature of 1 kilogram of water 1 degree Celsius. Sometimes the energy content of food is expressed in kilojoules (kj), a metric unit. One kcal equals 4.184 kj. So the Calorie on a food package is 1,000 times larger than the calorie used in chemistry and physics.

    The original method used to determine the number of kcals in a given food directly measured the energy it produced.The food was placed in a sealed container surrounded by water–an apparatus known as a bomb calorimeter. The food was completely burned and the resulting rise in water temperature was measured. This method is not frequently used today.

    https://www.scientificamerican.com/article/how-do-food-manufacturers/

    Are you saying that your concept of “information content” is like that? Perhaps it is these false analogies that you appeal to that have you confused about information.

    So I ask again, what exactly are you referring to when you assert that something “contains information.”? I say you don’t know, and so you’ve posed a meaningless question that no one can answer to your satisfaction.

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  12. Rumraket: And presumably that includes Nonlin who made the OP as also not knowing what he’s talking about?

    The OP makes far more sense than people are giving it credit for. But it is far simpler to toss insults around than to question what one believes to be true or admit that perhaps we don’t actually know as much as we pretend to know.

    Who actually felt insulted by the OP?

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  13. a relevant comment at UD

    Following Orgel:

    Speaking of a measure of complexity, not a measure of information.

    The “information content” of a structure is the minimum number of instructions needed to specify the structure.

    These instructions are not found in the structure itself. They are not contained in the structure. Tree rings are not instructions. If the “information content” is physical, where is it? Where does this “minimum number of instructions needed to specify the structure” reside?

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  14. Mung: Rumraket: Amount. Quantity. How much information there is. Like “caloric content” of some food. It has so many joules pr. gram.

    I’d like to see a similar thing done for functional DNA, like a protein coding gene of some length. How much functional information is that? I’m assuming we measure it in bits.

    But they are not the same. “Caloric content” refers to something physical. There is something in the food that can be converted by physical means into something else. Don’t you agree? How is that true of “information content”?

    It doesn’t matter that information is not exactly analogous to calories, the point is it can be measured out of some total mass. Calories per gram.

    We can measure how many calories some particular food contains. And we can measure information for a great number of things. Most obviously is my computer’s hard-drive and memory, which stores digital information. We measure it in bits.

    In an analogous way, I want to determine how much information some particular protein coding DNA-sequence contains. How many bits pr nucleotide?

    If somebody claimed that there is no way that process X could increase the energy content pr unit of mass of some particular food, we could test it by first measuring the energy content, then subjecting the food to the process, and measuring it again to see if it has more, less, or the same amount of calories.

    If creationists can’t actually calculate that for information, then creationists have no grounds for declaring that evolution can’t create information. Because only by testing the claim against observations, which means being able to measure how much information there is at some moment in time, versus a later moment in time after evolution has happened, can we determine whether more information was added, or deleted, or stayed the same.

    By dodging this SUPREMELY simple challenge, you are tacitly conceding that the creationist claim has ZERO merit. You can’t claim that process X can’t accomplish the creation of Y, if you have no way of measuring Y.

    This is the whole MathGrll debacle over again. You are all full of shitty excuses, it is pathetic to behold. On the one hand you wish to keep insisting that evolution can’t create information, on the other hand you do everything you can to avoid subjecting that claim to a concrete empirical test.

    Every single post you make in response that isn’t a formula for calculating the quantity of information in some functional stretch of DNA will be another big fat piece of evidence in favor of the conclusion that you are flailing, feeble hypocrites with nothing real to offer other than assertions you can’t support.

    You’ve been had. The gig is up. You are more transparent than intergalactic vacuum is to neutrino radiation. Frauds, biased frauds all of you.

    So I ask again, what exactly are you referring to when you assert that something “contains information.”?

    I don’t have to answer that, the person who claims that DNA contains information that evolution couldn’t possibly create is the one who needs to answer that. That’s why it’s ME who is asking for a way to meaure information. Because only then can the claim being made by creationists such as Nonlin who made the OP, be tested.

    Now stop dodging, and admit that you don’t know how to support the creationist claim, and therefore are not going to support it in the future, and will call out creationists who make it. Like Nonlin did.

    Or give a way to measure information content of DNA, so that we can test the claim that evolution can’t create it by doing before-and-after measurements on DNA sequences that have undergone evolutionary change.

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  15. Rumraket,

    In an analogous way, I want to determine how much information some particular protein coding DNA-sequence contains. How many bits pr nucleotide?

    gpuccio has devised a measurement for conserved proteins. Why don’t you start there?

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  16. colewd: gpuccio has devised a measurement for conserved proteins. Why don’t you start there?

    So if I give you the amino acid sequence of some particular protein, will you be able to calculate how many bits of information there is?

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  17. Rumraket,

    So if I give you the amino acid sequence of some particular protein, will you be able to calculate how many bits of information there is?

    With the caveat of an error factor; yes. He can make a measurement based on historical preservation of AA sequences. That is what his hypothesis is all about. Are you able to post at UD? If not I will have him post his method which he wrote in an op about.

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  18. colewd: With the caveat of an error factor; yes. He can make a measurement based on historical preservation of AA sequences.

    Yeah that makes very little sense. Why would historical preservation be a factor in determining how much information there is in a functional sequence?

    We could take a sequence that was designed by humans, like some enzyme used in an industrial product, which has no evolutionary relationships at all and therefore no conservation or history. Would Gpuccio then not be able to calculate how many bits of information there is in that designed sequence?

    it would seem fantastically strange to me if creationists claim only ID has the ability to create information, yet only be able to estimate how much there is for molecules with a demonstrable evolutionary history. That’s… that’s just… amazing.

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  19. Rumraket,

    Yeah that makes very little sense. Why would historical preservation be a factor in determining how much information there is in a functional sequence?

    Why don’t you learn his method first. There will be discussion about the error factor and that would be useful.

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  20. Corneel,

    I hope you can see now DNA repair and purifying selection are very different things.

    They are certainly different but they are both a head wind for evolution as they reduce variation. So does apoptosis which is a part of the cell cycle and initiated when DNA repair fails.

    When you look at an organism as a system functional variation needs to be minimized.

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  21. colewd: Yeah that makes very little sense. Why would historical preservation be a factor in determining how much information there is in a functional sequence?

    Why don’t you learn his method first.

    I understand his method, which is why I’m saying it doesn’t make sense. How would one calculate information content of a designed gene without any evolutionary history? He talks a lot about conservation as a factor to use in calculating the amount of information for some system, or sequence. But what if I want to calculate information for something designed?

    You know, an estimation of the amount of information in a designed and created gene before evolution.
    And then subject it to some evolution.
    And then calculate the amount of information after evolution.

    How would I go about doing the calculation for the “before” case, for a known-to-have-been-created-by-humans protein that doesn’t have an evolutionary history?

    I tried to look at Gpuccio’s “method”, and it made no sense.

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  22. colewd:
    They are certainly different but they are both a head wind for evolution as they reduce variation. So does apoptosis which is a part of the cell cycle and initiated when DNA repair fails.

    1. DNA repair prevents “erosion” of genes. Mutations cannot be too high or too many genes would be damaged and evolution would not be able to proceed. Some scientists back in the 60s determined how precise DNA duplication would have to be in order for evolution to proceed and the gained evolved features to persist. They found that DNA repair mechanisms kept DNA within appropriate ranges. You’ve said too many times that mutations would “erase the information.” Well, only if too high. This is where DNA repair comes into play. So, no, DNA repair is not a head wind for evolution, it’s a safeguard.

    2. Purifying selection doesn’t minimize variation, it’s but what happens when mutations are comparatively disadvantageous. Non-damaging variation goes on all right.

    3. Apoptosis doesn’t minimize variation either. For one, it’s cell-specific, not complete organism. For another, besides other functions, it only destroys damaged cells. Cells not showing the signs of damage that bring up apoptosis don’t go into apoptosis (obviously) regardless of the mutations they might carry.

    colewd:
    When you look at an organism as a system functional variation needs to be minimized.

    Not the functional variation Bill. It’s mis-functional variation that gets minimized.

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  23. Rumraket: It doesn’t matter that information is not exactly analogous to calories, the point is it can be measured out of some total mass. Calories per gram.

    We can measure how many calories some particular food contains. And we can measure information for a great number of things. Most obviously is my computer’s hard-drive and memory, which stores digital information. We measure it in bits.

    In an analogous way, I want to determine how much information some particular protein coding DNA-sequence contains. How many bits pr nucleotide?

    Sure it matters, I explained why and you even agree with what I wrote about calories. Now explain how the same holds true of information.

    What is the process for measuring “information content” that is analogous to measuring “calorie content.”

    If you can’t say why not just admit it?

    What do you do to your DNA string in order to find out how much informaiton content it has? Burn it and see what effect it has on the water temperature?

    You don’t get to claim they are analogous and then just wave your hands about as you have done.

    As for your hard drive, how do you determine how much information content it has and is that how complex you consider your hard drive?

    A 500MB hard drive is less complex than a 1000MB hard drive by half?

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  24. Rumraket: I understand his method, which is why I’m saying it doesn’t make sense.

    Brilliant. It makes no sense, but you understand it anyways.

    I think that’s the missing piece for me with evolution. Expecting it to make sense when I should just be able to understand it even if it doesn’t make sense.

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  25. Rumraket: Why would historical preservation be a factor in determining how much information there is in a functional sequence?

    Why would evolution preserve functional sequences indeed. Because we all know that untold billions of functional sequences must have come and gone throughout the history of life. Right?

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  26. Mung: Brilliant. It makes no sense, but you understand it anyways.

    I think that’s the missing piece for me with evolution. Expecting it to make sense when I should just be able to understand it even if it doesn’t make sense.

    I’m guessing you’re back here because they kicked you out of WoW for your pathetic trolling

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  27. Entropy,

    Not the functional variation Bill. It’s mis-functional variation that gets minimized.

    You are ignoring the problem of functional interdependence at the system level.

    Anything that stops change from a functional sequence is limiting variation. Purifying selection, DNA repair and apoptosis all do this.

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  28. colewd: You are ignoring the problem of functional interdependence at the system level.

    And that before the mis-functional variation was mis-functional it was functional.

    So what he really means is that one functional variant get replaced by a different functional variant. And the evidence gets erased. I love evolutionary theory.

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  29. colewd: Why don’t you learn his method first. There will be discussion about the error factor and that would be useful.

    A worked example would be helpful for comprehension. It makes no sense for others to perform a calculation he has devised, they will invariably get it wrong.

    Can you ask for a worked example? For the “before” and “after” case, obviously.

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  30. colewd: Anything that stops change from a functional sequence is limiting variation. Purifying selection, DNA repair and apoptosis all do this.

    And yet variation happens in living organisms. How many genetic mutations do you think you have?

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  31. OMagain,

    Can you ask for a worked example?

    Sure.

    And yet variation happens in living organisms. How many genetic mutations do you think you have?

    Not sure but I think I am a hair short of evolving into a next generation human:-)

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  32. Mung: Sure it matters, I explained why and you even agree with what I wrote about calories. Now explain how the same holds true of information.

    What is the process for measuring “information content” that is analogous to measuring “calorie content.”

    That’s what I’m asking. Nobody wants to give a sensible answer that can be used to test the claim that evolution can’t create information.

    The only thing offered so far is a calculation that involves an irrelevancy, so it doesn’t make sense.

    If you can’t say why not just admit it?

    I admit that I don’t know how creationists calculate information content of genes where that calculation can be used to support the claim that evolution can’t create information.

    This isn’t my problem, it’s a problem with creationists unwillingness to just provide a straightforward way of doing that.

    What do you do to your DNA string in order to find out how much informaiton content it has?

    That’s what I’m asking. Gpuccio had a suggestion, but it involves looking at how conserved some protein is across the tree of life. Why the hell would that be a factor that determines how much information is in the sequence? That doesn’t make sense, because then it becomes impossible to calculate the information content for a designed sequence with no evolutionary history. Which is fantastic!

    Burn it and see what effect it has on the water temperature?

    You don’t get to claim they are analogous and then just wave your hands about as you have done.

    I get to claim they are analogous in exactly the way they are analogous: There is some entity (DNA, or food), that is claimed to contain some attribute (information for DNA, calories for food).

    And creationists like Nonlin in the OP claims there is no way evolution can create information.

    In order to determine that, we have to be able to measure how much information there is in DNA, so we can then analyze whether DNA that has been undergoing evolution also changed the amount of information there is. In fact, creationists often claim that evolution can only preserve or destroy information, never create it. That must mean they have some way of determining how much there is, in order to be able to say that evolution has destroyed some of it. They must have a way of doing before-and-after measurements on DNA.

    I want to know what that method is, but nobody wants to give a shot at providing a method that makes sense.

    As for your hard drive, how do you determine how much information content it has

    I just look at the used space on my hard drive. It has a capacity for storage of information, and out of that total capacity, some of it is taken up and stores information.

    A 500MB hard drive is less complex than a 1000MB hard drive by half? and is that how complex you consider your hard drive?

    No, I don’t think complexity is identical with information content. I don’t much care for how to measure complexity (though I can suggest ways to do that), right now I’m interested in seeing whether someone can give a way to calculate information content of DNA so that I can subject Nonlin’s and similar creationist claims to a test.

    But creationists are manifestly desperate to avoid that test taking place. I think I know why.

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  33. Mung: Brilliant. It makes no sense, but you understand it anyways.

    I understand how he does his calculation, but that the calculation doesn’t make sense because it involves a factor that should be completely irrelevant.

    The information content in some particular gene can’t depend on how conserved it is across the tree of life, because then designed genes, for example for enzymes used in industrial chemistry, have an impossible to determine information content as they don’t exist anywhere in life.

    That’d be like saying that the amount of information in a book depends on whether other people who own the book has edited it and by how much.

    How does that make sense? It doesn’t.

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  34. Mung: Rumraket: Why would historical preservation be a factor in determining how much information there is in a functional sequence?

    Why would evolution preserve functional sequences indeed.

    Because changes to them are overwhelmingly more likely to have a significant negative effect on reproductive success because their function is deeply embedded in a larger framework where many other important functions depend on them.

    Why would that have anything to do with how much information there is in a sequence? If I create an enzyme by design, for use in some industrial chemical process, it will have no evolutionary history and only exist in one entity. So it is basically nonexistent across the tree of life, except the one organism that I happen give this gene to. Does this gene have less information, or more information, or the same amount of information, if it gets horizontally transferred to other species on the tree of life? Why?

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  35. Entropy: 1. DNA repair prevents “erosion” of genes.

    I should have corrected this earlier when Bill brought it up first.

    Actually, DNA repair deals with fixing physical damage to DNA strands, like a double strand breaks. This process can actually lead to mutation, rather than correcting them as it, among oher things, can incorrectly splice together different fragments of DNA.

    What Bill is thinking of but used the wrong term for, is “proofreading” mechanisms that scan for basepair mismatches or deaminations, and “correct” them. In any case, what I stated earlier still applies. This proofreading mechanism isn’t perfect, mistakes still slip through the net so to speak. There is no conflict implied between evolution as a historical process, and the reality of proofreading mechanisms combined with purifying selection.

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  36. Rumraket,

    I understand how he does his calculation, but that the calculation doesn’t make sense because it involves a factor that should be completely irrelevant.

    The information content in some particular gene can’t depend on how conserved it is across the tree of life, because then designed genes, for example for enzymes used in industrial chemistry, have an impossible to determine information content as they don’t exist anywhere in life.

    That’d be like saying that the amount of information in a book depends on whether other people who own the book has edited it and by how much.

    How does that make sense? It doesn’t.

    He is not measuring the information content of any gene. He is measuring the information content of historically preserved genes. Amino acid positions that were preserved over 400 million years. The calculation is not perfect but it is a great start.

    O Magain requested he share his work. I have made this request at UD so I hope you take a genuine look at it.

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  37. colewd,

    Can you give me a tip? You seem like a reasonable, educated human being…
    How do you try to, if any, to convince people who do not what to be convinced?

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  38. At subatomic level, “information” becomes “real” ONLY” when there is observer…Evolution must be the observer she must be one of “them” lol

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  39. Rumraket,

    This proofreading mechanism isn’t perfect, mistakes still slip through the net so to speak. There is no conflict implied between evolution as a historical process, and the reality of proofreading mechanisms combined with purifying selection.

    If we disabled this mechanism (DNA mismatch repair) what do you think would happen?

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  40. J-Mac,

    How do you try to, if any, to convince people who do not what to be convinced?

    People with strong world-views are not going to change with even very convincing arguments unless one happens to trigger something.

    Arguing with someone that completely agrees with you, on the other hand, can be boring:-)

    If you put your arguments to a sincere test and they stand up to reasonable criticism then you probably have a solid position.

    The world (media, educational systems and political leadership) is trying to indoctrinate all of us so I admire anyone who comes here and puts their basic beliefs to the test.

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  41. colewd:
    J-Mac,

    People with strong world-views are not going to change with even very convincing arguments unless one happens to trigger something.

    Arguing with someone that completely agrees with you, on the other hand, can be boring:-)

    If you put your arguments to a sincere test and they stand up to reasonable criticism then you probably have a solid position.

    The world (media, educational systems and political leadership) is trying to indoctrinate all of us so I admire anyone who comes here and puts their basic beliefs to the test.

    Well, Great! So, what’s your purpose here?

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  42. J-Mac,

    To challenge my own thoughts and arguments and shake them out. My original reason was to find a partner for a research project but that need went away. I find the discussions on philosophy very interesting as I am a complete neophyte in that area.

    When I see the opposition use logical fallacies like straight assertions, circular reasoning or ad hominem arguments as challenges then I know I am on the right track. I think challenging your own ideas and world-view in general is a good idea. Mine has certainly changed over the last 3 years.

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  43. colewd: logical fallacies

    Hey coled,
    What are the logical fallacies?
    I hope that English is not your first language.. It isn’t even my third… I think…lol

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  44. colewd:
    You are ignoring the problem of functional interdependence at the system level.

    No, I’m not.

    colewd:
    Anything that stops change from a functional sequence is limiting variation.Purifying selection, DNA repair and apoptosis all do this.

    I really hate when you do this. You just ignored everything I explained (or it went way over your head, and you’d rather not admit to it). So I’ll leave it here.

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  45. OMagain,

    Here is Gpuccio’s reply.

    As said, I use conservation through long evolutionary times to measure functional constraint.

    The alpha and beta chains of ATP synthase have been hughly conserved for maybe billions of years. That is a very high evolutionary time.

    The bitscore between the human form and the bacterial form is a very good measure of how much the sequence is conserved, and therefore of its functional constraint. It expresses the probability of finding that level of homology by chance (Indeed, the probability is the E value, which is directly related to the bitscore. Unfortunately, the E-value is set to 0 when it becomes lower than some threshold, and therefore cannot be used as a measure for the high levels of functional information we are discussing here).

    Therefore, the bitscore is an indirect measure of the functional information in the sequence.

    As said, the two chains in ATP synthase have more than 1000 bits of functional information, as evaluated by the bitscore between bacteria and humans.

    As explained many times, these two sequences have been exposed to at least 1-2 billion years of neutral variation since the split of bacteria from human lineage. More than enough to change all that could change. 400 million years are more than enough for that, as many times debated. 1-2 billion years are really much more than enough.

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  46. colewd:
    If we disabled this mechanism (DNA mismatch repair) what do you think would happen?

    I explained this to you Bill, there would be “meltdown” rather than evolution. Truly Bill, am I talking to a wall?

    It’s frustrating to explain things to you and get an “answer” that shows lack of reading (for comprehension?), and then see you posing a question to someone else that I already answered.

    So, getting this straight. You either don’t read our answers, or you don’t understand them. Because you neither read, nor understand the answers, you think they must surely be logical fallacies and that means you’re on the right track. Challenging your own thoughts all right.

    I should not have kept reading your comments. It’s horrifyingly disappointing.

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  47. colewd: As explained many times, these two sequences have been exposed to at least 1-2 billion years of neutral variation since the split of bacteria from human lineage. More than enough to change all that could change. 400 million years are more than enough for that, as many times debated. 1-2 billion years are really much more than enough.

    Ridiculous. There’s wouldn’t be any significant sequence similarity if it had undergone 2 billion years of neutral evolution.
    Puccio is forced to say that because his pathetic negative argument relies on there being no functional pathway in the transition, despite evidence to the contrary.

    Why would the designer come up with a sequence for vertebrates and bacteria that just happens to be in the vicinity of sequence space of the ancestral one if he had enough time and resources to explore the entire search space according to Puccio? Why make it look like it wasn’t neutral evolution at all?

    Classic case of imagining a non existing barrier and proposing a magical solution that just makes it look like there was no barrier to begin with

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  48. colewd: They are certainly different but they are both a head wind for evolution as they reduce variation. So does apoptosis which is a part of the cell cycle and initiated when DNA repair fails.

    Yes they limit the amount of genetic variation, but as has been pointed out by several posters, neutral (and beneficial) variation accrues nevertheless. Humans have an enormous amount of genetic variation (an estimated number of ~10 million SNPs for example). Please note that, compared to other organisms, humans score at the low end in terms of genetic variation.

    colewd: When you look at an organism as a system functional variation needs to be minimized.

    … which, by your own admission, is exactly what selection does. So are you ready to withdraw your statement:

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

    Adaptations are NOT fixed through serendipity but by the requirement that “functional variation needs to be minimized”, which means tossing out the ancestral (less fit) alleles. This is the same process that will prevent that information from being lost, namely selection in its purifying role. Bill Basener and John Sanford are wrong. Time to get your story straight, Bill.

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  49. J-Mac: Can you give me a tip? You seem like a reasonable, educated human being…
    How do you try to, if any, to convince people who do not what to be convinced?

    Why, you just make content-free condescending remarks in the thread where they can be read by all that you wish to convince. Didn’t you know?

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