Computing, AI, Cybernetics and Mechatronics Design inference Intelligent Design

Does information theory support design in nature?

Spread the love

Eric Holloway argues at Mind Matters that design theorist William Dembski makes a convincing case, using accepted information theory principles relevant to computer science:

When I first began to look into intelligent design (ID) theory while I was considering becoming an atheist, I was struck by Bill Dembski’s claim that ID could be demonstrated mathematically through information theory. A number of authors who were experts in computer science and information theory disagreed with Dembski’s argument. They offered two criticisms: that he did not provide enough details to make the argument coherent and that he was making claims that were at odds with established information theory.

In online discussions, I pressed a number of them, including Jeffrey Shallit, Tom English, Joe Felsenstein, and Joshua Swamidass. I also read a number of their articles. But I have not been able to discover a precise reason why they think Dembski is wrong. Ironically, they actually tend to agree with Dembski when the topic lies within their respective realms of expertise. For example, in his rebuttal Shallit considered an idea which is very similar to the ID concept of “algorithmic specified complexity”. The critics tended to pounce when addressing Dembski’s claims outside their realms of expertise.

To better understand intelligent design’s relationship to information theory and thus get to the root of the controversy, I spent two and a half years studying information theory and associated topics during PhD studies with one of Dembski’s co-authors, Robert Marks. I expected to get some clarity on the theorems that would contradict Dembski’s argument. Instead, I found the opposite.

Intelligent design theory is sometimes said to lack any practical application. One straightforward application is that, because intelligence can create information and computation cannot, human interaction will improve computational performance.
More.

Also: at Mind Matters:

Would Google be happier if America were run more like China? This might be a good time to ask. A leaked internal discussion document, the “Cultural Context Report” (March 2018), admits a “shift toward censorship.” It characterizes free speech as a “utopian narrative,” pointing out that “As the tech companies have grown more dominant on the global stage, their intrinsically American values have come into conflict with some of the values and norms of other countries.”

Facebook’s old motto was “Move fast and break things.” With the current advertising scandal, it might be breaking itself A tech consultant sums up the problem, “Sadly Facebook didn’t realize is that moving fast can break things…”

AI computer chips made simple Jonathan Bartlett: The artificial intelligence chips that run your computer are not especially difficult to understand. Increasingly, companies are integrating“AI chips” into their hardware products. What are these things, what do they do that is so special, and how are they being used?

The $60 billion-dollar medical data market is coming under scrutiny As a patient, you do not own the data and are not as anonymous as you think. Data management companies can come to know a great deal about you; they just don’t know your name—unless, of course, there is a breach of some kind. Time Magazine reported in 2017 that “Researchers have already re-identified people from anonymized profiles from hospital exit records, lists of Netflix customers, AOL online searchers, even GPS data of New York City taxi rides.” One would expect detailed medical data to be even more revelatory.

George Gilder explains what’s wrong with “Google Marxism”
In discussion with Mark Levin, host of Life, Liberty & Levin, on Fox TV: Marx’s great error, his real mistake, was to imagine that the industrial revolution of the 19th century, all those railways and “dark, satanic mills” and factories and turbine and the beginning of electricity represented the final human achievement in productivity so in the future what would matter is not the creation of wealth but the redistribution of wealth.

Do we just imagine design in nature? Or is seeing design fundamental to discovering and using nature’s secrets? Michael Egnor reflects on the way in which the 2018 Nobel Prize in Chemistry has so often gone to those who intuit or impose desire or seek the purpose of things

600 Replies to “Does information theory support design in nature?

  1. 1
    daveS says:

    EricMH,

    When I first began to look into intelligent design (ID) theory while I was considering becoming an atheist, I was struck by Bill Dembski’s claim that ID could be demonstrated mathematically through information theory.

    Slightly tangential, but do you think if you hadn’t studied information theory (and perhaps related fields), that you would likely be an atheist today?

    I’m asking because I believe the majority of Christians I know did not get there via mathematics and the sciences, but rather through studying the bible, history, perhaps reflecting on sermons they had heard in church, witnessing how Christians live their lives, experiencing miracles, etc.

  2. 2
    EricMH says:

    @daveS, it’s hard to say exactly what route I would have gone. But ID did have a big influence on the direction I did go. However, I noticed the things that many other Christians found pretty convincing were not as effective for me. Definitely none of the emotional appeals worked for me, nor the good lives lived by Christians. The accounts of miracles were a bit more convincing, and I attended Pentecostal churches until I became Catholic, and heard a number of fascinating stories from people I trust, though never directly witnessed a miracle. I was willing to reject all of that if it was false. I really wanted something absolute like mathematics and testable like science. The big draw of ID is that it says religious claims fit into those categories.

  3. 3
    Mung says:

    If Christianity required math I’d be going to hell!

  4. 4
    daveS says:

    Thanks for that, EricMH.

  5. 5
  6. 6
    EricMH says:

    Shallit says entropy is information. Same with Swamidass. This appears to be a misreading of information theory to me. Shannon proposes -log p as a measure of information, and E[-log p] as the expected information from a random variable, which Shannon calls entropy or uncertainty.

    But a measurement is not the thing being measured. For example, a pound is a measure of fruit, but a pound is not a fruit. So, just because a source has high entropy does not mean it has a large amount of information. It’d be like saying because my bag can hold 10 pounds, it has 10 pounds of fruit. The capacity does not dictate the content.

  7. 7
    Tom Robbins says:

    I completely understand the more intellectual route to Christianity. I always believed in some kind of creator and I used the word God at an early age. My Mom at the time was a unitarian, and my father an obvious agnostic, who would only consider an impersonal force that could have a type of intelligence that got things going – but he was doubtful of this. But my fathers thinking was very different than mine, I simply could not, and would not believe, that suddenly I am here in this moment, having these experiences, all due to some kind of dumb luck, and for no purpose.

    We studied both neo-darwinism and Gould’s Punctuated equilibrium, but even though I understood the material, understood what the claims were, I knew instinctively that what I was being taught was not science, but a more of a terribly oversimplified story, much like you would expect from a creation story of some isolated tribe, only with a lot of words that sounded scientific. I noticed right off the bat that the word Evolution was used way too much to explain the theory of evolution, as in “Evolutionary processes selected for this or that” and that somehow Evolution was creative, and it was always talked about as if it could think ahead, even though the theory does not allow it.

    I recall reading a story about how a squirrel became a flying squirrel by Richard Dawkins – he was a decent writer, but his description where the flap of skin under the arm and shoulder, mutated to be larger and more flabby, so it could now survive a fall from a tree from hight X, then it grew even larger due to more lucky mutations, and it could then survive a fall from height X+1 and so matted more often!! I was like you have to be joking – this from the great Richard Dawkins!!?? I honestly think you have to be an idiot to believe this is how life diversified.
    I went on to learn about quantum physics, and all the attempt to discredit the observer effect have failed, so it became very clear to me that MIND is primary, matter/space and time were secondary.

    Then looking inside the cell, at DNA, and claiming that it just “decided” to develop a mechanism to copy its data and store immaterial information to construct and build breaking all laws of entropy and the law of common damn sense! Also it happened to “decide” to make this elaborate and elegant system to copy its DNA and pull half of it to either side of itself, and then divide?? Why in the world would dumb matter behave in this way? The answer is simple, it can’t and it would not. Some people still think given enough time ANYTHING CAN HAPPEN – two big problems here – anything keeps happening over a limited amount of time in just the right way to create and maintain life? AND the fact that ONLY things that are possible through chemistry and physics can happen over time, it is completly false to say given the laws of our universe, and enough time, anything can happen – NO, only thing that are allowed by physical laws can happen given enough time – not anything. And organic matter is so fragile to begin with I knew they were off their rocker.

    So bottom line this, plus the historical facts of christianity + reading the words of Jesus, made me get on my knees and say I believe in you, I am your child, forgive me. And it makes one stronger by letting go of control, and serving, not weaker… blah, blah.

  8. 8
    Bob O'H says:

    EricMH @ 6 – I wonder if that’s not a mis-reading, but a different interpretation. From what you write, you think that information is something “out there”, i.e. independent of our science and observations. But I look on information as something purely a part of human science. it’s a statistics we use to summarise a lot of complexity. It’s convenient and useful, but is purely part of the map, not the landscape. I don’t know if Shallit and Swarmidass think the same thing, but if they do that might suggest a more fundamental difference of opinion.

  9. 9
    Nonlin.org says:

    EricMH @ 6

    Indeed, confusing entropy with information is very bad especially when you claim to be an expert. Even worse is that these “experts” don’t know the difference between information, data, and media.

    BTW, I also disagree with Robert Marks’ claim that a picture of Mt. Rushmore contains more information than one of Mt. Fuji. That’s because information is abstract and user dependent. Does a circle have more, less, or same information as a square?

    A lot of confusion comes from Shannon himself calling his theory “of information” when in fact he only cared about data integrity, not information.

  10. 10
    Nonlin.org says:

    EricMH @ 6

    And of course you’re wrong too: entropy is not a property of information, but of data. For instance, the idea of ‘a circle’ has no entropy, but the hex representation of its character string does.

  11. 11
    PaoloV says:

    Interesting discussion.

  12. 12
    daveS says:

    Bob O’H,

    From what you write, you think that information is something “out there”, i.e. independent of our science and observations. But I look on information as something purely a part of human science. it’s a statistics we use to summarise a lot of complexity. It’s convenient and useful, but is purely part of the map, not the landscape.

    I think this clarifies some things for me.

    Is there some way to decide which view (if either) is correct?

  13. 13
    Mung says:

    daveS

    Is there some way to decide which view (if either) is correct?

    It’s not something that can be settled by science. 🙂

    And I guess it depends on whether you prefer clarity to nonsense.

    In one view you can receive a “message” that can be total gibberish and they will tell you they can measure the “information content” of the message.

    Simple intuition tells you that is nonsensical.

    Shannon and Weaver were quite explicit about his measure, but the so-called experts ignore that. Presumably because they know better than Shannon.

  14. 14
    Mung says:

    EricMH:

    Shannon proposes -log p as a measure of information

    1.) Where does he do that?
    2.) -log p of what?

    Can you help me decipher this?

    Swamidass:

    Do you realize that -log p = H (information equals entropy)? This is why, for example, people use the formula p=2-Hp = 2^{-H}, the probability of a message is the negative exponential of its entropy.

    Thanks

  15. 15
    daveS says:

    Mung,

    And I guess it depends on whether you prefer clarity to nonsense.

    In one view you can receive a “message” that can be total gibberish and they will tell you they can measure the “information content” of the message.

    Simple intuition tells you that is nonsensical.

    I would agree (based only on my intuition) that the measurement of the “information content” would not tell me anything about the meaning (or lack of meaning in this case) in the message.

    On the other hand, couldn’t some of these information statistics tell me whether the gibberish at least had some sort of structure?

    Perhaps the “messages” we’re looking at are more like “signs”, where there is no text being transmitted, but rather just improbable structures, such crop circles or something.

  16. 16
    Mung says:

    daveS:

    On the other hand, couldn’t some of these information statistics tell me whether the gibberish at least had some sort of structure?

    Perhaps some. But in general the measure defined by Shannon is a measure across a probability distribution. If you model the message as a distribution you can measure the “amount of information” associated with that distribution.

    And that has to do with the frequencies or probabilities of symbols and not with the actual content of the message. So “information content” is an unfortunate misnomer.

  17. 17
    Axel says:

    If intellectual integrity were a necessary criterion – perhaps even acceptable criterion – for teaching most tertiary studies, surely the academic establishment would be decimated.

    But isn’t it curious, however understandable, how ‘light’ as well as being a physical reality, is used metaphorically for intellectual illumination, and widely identified either with the divine. Surely, most of all in Judaeo-Christianity.

    The latter, bearing in mind, particularly that, via their Baptism, Christians are, at least, embryonically, already inducted into the Mystical Body of Christ, the True Vine.

    Moreover, we know that, while light photons interact with space-time, their proper framework of reference has to be outside of space-time and absolute in relation to it.

    I believe I read here that the origin of all sub-atomic particles has been found to be external to space-time. Is that right ?

  18. 18
    Axel says:

    ‘Then looking inside the cell, at DNA, and claiming that it just “decided” to develop a mechanism to copy its data and store immaterial information to construct and build breaking all laws of entropy and the law of common damn sense! Also it happened to “decide” to make this elaborate and elegant system to copy its DNA and pull half of it to either side of itself, and then divide?? Why in the world would dumb matter behave in this way? The answer is simple, it can’t and it would not. Some people still think given enough time ANYTHING CAN HAPPEN – two big problems here – anything keeps happening over a limited amount of time in just the right way to create and maintain life? AND the fact that ONLY things that are possible through chemistry and physics can happen over time, it is completly false to say given the laws of our universe, and enough time, anything can happen – NO, only thing that are allowed by physical laws can happen given enough time – not anything. And organic matter is so fragile to begin with I knew they were off their rocker.’
    – Tom Robbins

    More LOL, surreal, knockabout humour from the atheists, eh, Tom ? How do they get away with it ? I remember reading that Pauli was appalled that they hadn’t even performed any kind of calculations in support of this barmy ‘promissory’ twaddle.

    I believe I read that just to perform some fiddling little ‘transmogrification’ of matter by a fortuitous interaction of protein ‘gizmeters’ (sorry, can’t remember the name), would require greater odds against it occurring than there are SUBATOMIC particles in the known universe.

    I suppose Pauli wold be familiar enough with that tribe to not be shocked to learn that they still hadn’t produced any kind of supporting calculations !

  19. 19
    EricMH says:

    Bob O’H @ 8, it is a semantic argument masquerading as a logical argument. The argument goes like this:

    ID claims there is a quantifiable difference between the output of a random coin and the output of a designing intelligence, and we call this difference information (CSI).

    When infotropy crowd sees the ID argument, they say:

    1. Entropy is information
    2. Flipping a coin generates a lot of entropy
    3. Therefore, flipping a coin generates a lot of information
    4. Therefore, all the information in DNA can be generated by flipping a coin

    Both sides are talking about apples and oranges, but the infotropy crowd declares victory by renaming apples oranges.

  20. 20
    EricMH says:

    @Mung, from Shannon’s paper:

    If the number of messages in the set is finite then this number or any monotonic function of this number can be regarded as a measure of the information produced when one message is chosen from the set, all choices being equally likely. As was pointed out by Hartley the most natural choice is the logarithmic function. Although this definition must be generalized considerably when we consider the influence of the statistics of the message and when we have a continuous range of messages, we will in all cases use an essentially logarithmic measure.

  21. 21
    EricMH says:

    @daveS, I think more important than arguing about definitions is looking at the mathematics. Is there a way to quantify order, or is one person’s order another person’s disorder? This question is answered by Kolmogorov complexity, K(X). Orderly objects are highly compressible, disorderly objects are incompressible.

    A second question is: what about things like crystals that are highly ordered? A crystal is highly ordered, but because it is naturally produced that way, the object has high probability. So, we want an object that has low probability (i.e. not a crystal).

    Thus, we arrive at the quantity we want: an object that has a low probability and low Kolmogorov complexity. This is CSI.

    We measure it by CSI(X) = -log p(X) – K(X).

    CSI gets a bit more sophisticated, but the above is the basic idea. The main takeaway is CSI is an objective, quantifiable property of the object.

  22. 22
    daveS says:

    EricMH,

    I agree with you to some extent, at least for certain statistics. For example, the max girth of a rectangular box is the sum of its length and girth, and that is objective and quantifiable. Whether it exists “out there” in the box rather than in our minds, I’ll have to think about.

    Now for CSI, obviously that would be a bit more difficult to calculate. Consider finding the CSI of a 1 3/8-inch smooth paper clip. You would need to find the probability of it arising, I guess, under certain conditions*, as well as an estimate of its Kolmogorov complexity. Is that feasible?

    *Edit: I guess that means it depends partly on things outside the actual paper clip; the laws of physics, the history of the universe, etc?

  23. 23
    EricMH says:

    @daveS, there are two concerns here that tend to get conflated. First, whether we can measure something or not does not have the measurement. There could be a 10 pound rock on some distant planet we will never reach, and thus never be able to measure it. But, the rock is still 10 pounds. Same with CSI. It is an objective property of an object, regardless of whether we can measure it or not.

    With the paperclip, we’d first determine whether metals have inherent properties that turn them into paperclip shapes. If not, then the probability of paperclips spontaneously forming out of metal would be very small. Additionally, the paperclip is a shape that can be concisely described. Thus, it has a lot of CSI.

    Back with Shannon information, say the source is a uniform distribution over letters. So, LGCRUIB has the same Shannon information as ROSEBUD. However, the latter word is meaningful but the first word is gibberish. This shows Shannon information is a measure of informational capacity and not of informational content.

  24. 24
    daveS says:

    EricMH,

    Yes, there are indeed two distinct issues here. Despite my comment about feasibility (which is really irrelevant), I’m mostly interested in whether things such as paper clips have CSI in them or whether it’s part of the “map” as Bob O’H states.

    In order to (in principle) compute CSI, I think at least we would have to specify what initial conditions are assumed in the probability calculation. That is, we would need to specify “X” in: P(paper clips spontaneously forming | X).

    And since the initial conditions are external to the paper clip, this probability depends on things external to the paper clip.

    I agree that the shape of the paper clip is easily and concisely described mathematically, and if the length of a description of the shape is all we’re after, that quantity doesn’t depend on external factors.

  25. 25
    daveS says:

    PS to #24:

    I do agree that with some stipulations, then the CSI of the paper clip would have an objective, quantifiable value. That is, it would “exist” uniquely, as does the max girth of a rectangular box.

  26. 26
    EricMH says:

    @daveS, yes that’s a good question. All definitions of information measures I know of are in reference to some possible generating source. Shannon uses a random process. Kolmogorov uses a Turing machine. So, the external reference seems inescapable, at least within current theory.

    On the other hand, all the external definitions are usually related to an intrinsic property of the object: how many parts it has. In general, the more parts, the more information capacity. The second aspect is the arrangement of the parts. Certain arrangements possess more information content than others.

    The closest I’ve seen to an entirely intrinsic definition of information content is the Kolmogorov minimal sufficient statistic, which separates the Kolmogorov complexity of an object into noise and signal. It still is defined in reference to an external Turing machine, however.

    All that being said, I don’t think requiring an external reference is a mark against information measures. Every metric I can think of is in reference to some external reference. Measurement, in general, is about the relationship between two things. So, if external reference is a problem for information theory, it is a problem for every form of measurement we have.

  27. 27
    Bob O'H says:

    EricMH @ 23 –

    [CSI] is an objective property of an object, regardless of whether we can measure it or not.

    But the specification in CSI is done by people, is it not? So how do you make that objective? If the specification is defined in two ways by two different researchers (if they need names, I guess we can call them Bob and Bill) and they are different, which is the property of the object?

  28. 28
    Mung says:

    gizmeter. i love it!

  29. 29
    Mung says:

    infotropy – love that one too!

  30. 30
    Mung says:

    @EricMH. Thanks for the quote from Shannon.

    If the number of messages in the set is finite then this number or any monotonic function of this number can be regarded as a measure of the information produced when one message is chosen from the set, all choices being equally likely.

    He is talking about the number of messages. Not about the probability of a given message. when he says “this number” he is talking abut the number of messages, not their probability. This is the mistake that Swamidass makes.

    Given -log p, what does the p refer to? If it does not refer to the number of messages then it’s not an information measure as defined by Shannon.

    When I see -log p, to me, the p stands for a probability. What is it the probability of?

    My point here is that you wrote:

    Shannon proposes -log p as a measure of information

    I just don’t see that. What am i missing?

  31. 31
    Mung says:

    What happened to the ability to edit posts?

  32. 32
    Mung says:

    EricMH:

    Back with Shannon information, say the source is a uniform distribution over letters. So, LGCRUIB has the same Shannon information as ROSEBUD. However, the latter word is meaningful but the first word is gibberish. This shows Shannon information is a measure of informational capacity and not of informational content.

    Shannon information is a measure of informational capacity of what? The source?

    Respectfully, you are adding to the confusion. 🙂

    So we have a probability distribution. On this we agree. Shannon Information is a measure across a probability distribution.

    You are making it sound like Shannon Information has something to do with the message content. The Shannon Information is the same regardless of which message is selected. It has absolutely nothing to do with their content.

    Now given that the SMI has to do with probability distributions and not objects, it is mistaken to equate it with the “information content” of any object.

  33. 33
    EricMH says:

    @Bob O’H I agree that if specification is subjective, then confirmation bias becomes a problem. Two points: A) specification does not need to be done by people, and B) even if it is subjective, as long as the specification is independent from the event the math still works.

    @Mung, I am stating exactly what Shannon says at the beginning of his paper. What I am saying is that Shannon information is an upper bound on how much actual information the message can contain. A message of 100 words can contain much more information than a message of 4 letters. Likewise, a probabilistic source with high entropy can transmit much more information than one with low entropy. That’s the point of entropy in communication systems, maximizing entropy maximizes information transmission capacity.

    But you are right, the entropy measure itself says nothing at all about whether the channel capacity is filled with meaningful messages or random gibberish. All it does is put an upper limit on what can be transmitted.

    Regarding SMI, I don’t refer to SMI, I refer to algorithmic mutual information. Algorithmic information was formulated to deal with your objection, it concerns specific objects, i.e. bitstrings. That is the specification term in CSI: it is using algorithmic information to describe the specific event.

  34. 34
    Bob O'H says:

    As long as the specification is being done by someone (or thing), that surely means CSI can’t be an intrinsic property of an item: it is a measure being placed onto it by the specification. If another specification is used, the CSI could be different.

  35. 35
    Axel says:

    ‘Gizmeter’ tickled me, too, Esteemed Mung. ‘Gizmo’ is kinda dismissively cheap and gimcrack in very intention ; whereas, ‘gizmeter’ has a certain gravitas about it, doesn’t it ? Unashamedly polysyllabic and quite technical-sounding. Like my fraudulent username, Axel.

  36. 36
    EricMH says:

    @Bob O’H, With many possible specifications that are independent from the event, the one to pick is the one that maximizes CSI. That would be the closest to the true value.

  37. 37
    Bob O'H says:

    Right, so as I (and BIll) are doing the specification, we can create these so that each specification is one configuration of the data, and the whole set of configurations is covered. That makes life easy.

    Except that it means that random processes can generate CSI, because they generate one pattern in our specification.

    So if you don’t want Bill to be all smug (because it’ll be his specification that wins: he’s from Lubbock, and is pretty handy with a gun), you have to have some way of delimiting which specifications are possible, and this has to be visible (in some sense) to nature, otherwise the true value will be the maximum over all possibilities.

  38. 38
    gpuccio says:

    Bob O’H at #34:

    “As long as the specification is being done by someone (or thing), that surely means CSI can’t be an intrinsic property of an item: it is a measure being placed onto it by the specification. If another specification is used, the CSI could be different.”

    I have not followed the discussion here, but of course I agree with that.

    Functional complexity is linked to the defined function, not to the object itself. But it is exhibited by the object, for that function, if the object can implement the function as defined.

  39. 39
    Bob O'H says:

    Functional complexity is linked to the defined function, not to the object itself.

    That’s different from what Eric is arguing, and is closer to how I would view things (i.e. functional complexity is something we can calculate, and we can assign that value to an object). I guess this means that functional complexity is different from CSI, or different people in the ID community have different views on this.

  40. 40
    Bob O'H says:

    Aagh, forgot a / 🙁

  41. 41
    Mung says:

    Where can I get me a gizmeter? I assume it can measure anything at all? Can I replace my infometer with a gizmeter?

  42. 42
    gpuccio says:

    Bob O’H:

    “I guess this means that functional complexity is different from CSI, or different people in the ID community have different views on this.”

    Maybe. I have always had some difficulties with some of Dembski’s final ideas about specification. But the basic idea, that only design can generate some specific type of pattern, remains the same.

    I think that FC is just a subset of CSI. The subset where the specification is done by defining a function.

    I am convinced that that form is the simplest way to deal with complexity in the biological world. It allows to infer design from a purely empirical point of view.

    Probably Dembski has been pursuing a more general theory of CSI, a mathemathical theory that explains the foundations of the concept. That’s fine with me, but I cannot really judge if he has succeeded.

    For me, the empirical definition and the empirical design inference work perfectly well, and that’s what I am interested in.

  43. 43
    gpuccio says:

    Bob O’H:

    Another important point is that, with functional specification as I define it, there is no need to have one value of CSI for an object, be it the highest or anything else.

    It’s just enough that the object can implement at least one function that is complex enough (for example, beyond the 500 bit threshold). That’s enough to infer design for the object.

  44. 44
    Mung says:

    EricMH,

    There is a lack of precision in what you write that I personally find frustrating. 🙂

    Shannon’s measure of Information (SMI) can be applied to any probability distribution. It is far more general than you seem to give it credit for. Communication channels and message lengths have nothing to do with it.

    Shannon information is not an upper bound on how much information the message can contain.

    But you are right, the entropy measure itself says nothing at all about whether the channel capacity is filled with meaningful messages or random gibberish.

    That’s not even what I said. How did channel capacity enter into it? I thought we were talking about specific messages and their “information content.”

    All it does is put an upper limit on what can be transmitted.

    I’ll admit that I don’t understand this.

    A message of 100 words can contain much more information than a message of 4 letters.

    And I say that a message of four letters can contain much more information than a message of 100 words.

    Forget all about messages, meaning, gibberish, communications systems, channel capacity, transmission and all that. Wipe the slate of all that.

    Define a probability distribution. Given any distribution you can calculate the Shannon entropy (SMI). Everything needs to start with that basic understanding of what SMI has as its referent. Probability distributions.

    Not messages. Not message content. Not communications. All that is just the context in which Shannon derived his measure.

  45. 45
    Nonlin.org says:

    The so-called experts miss some basic facts about information:
    1. ‘Information’, ‘data’ and ‘media’ are distinct concepts
    2. Information is abstract and 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
    http://nonlin.org/biological-information/

  46. 46
    Nonlin.org says:

    Because the so-called experts miss so much, they make incorrect claims like:

    “Information is entropy”, Swamidass – WRONG, entropy is a propriety of data and has nothing to do with information

    “There’s more information in a picture of Mt. Rushmore than of Mt. Fuji”, Robert Marks – WRONG, we measure data, not information which is abstract.

    “White noise picture contains information in an amount that is also affected by resolution, size, compression, and other factors”, Jeffrey Shallit – WRONG, information is user dependent and of course there’s none in white noise.

    “We must detect design by evaluating the amount of functional information”, gpuccio – WRONG, information is not quantifiable (only data is) and design must be inferred from regularity, not information (see art)

    “Information is data”, Leonard Susskind – WRONG, see question at 1hr 15 min
    https://www.youtube.com/watch?v=HIJ44AtCCi8

    “Entropy measures information”, Eric M. Holloway – WRONG, entropy measures data, not information

    etc. etc.

  47. 47
    EricMH says:

    @Bob O’H humans create the metric, but the measurement is of something objective. E.g. humans invented the meter, but meters are a measurement of an objective property of an object. Same with CSI. Humans invent a specification, but it is still measuring an objective property.

    The key to avoid the dilemma you present is the specification must be independent of the event. If we just enumerate all possible specifications, and pick the one that matches the event, then the specification is no longer independent from the event. As such, the set of valid specifications has to be a subset of the possible specifications. Incidentally, this is how the field of machine learning selects a model that fits the data. The scenario you outline is called “overfitting” when the model space contains every possible permutation, so essentially the model is just the data itself, and not an abstraction.

    @Nonlin.org, I agree there is a difference between the abstract idea (information) and some physical object (data). Your terms seem more correct, because physical objects are not the same as abstract entities, and when we calculate SMI we are just measuring physical objects.

    @Mung, I apologize for lack of precision. How about we start with a uniform distribution over the 26 English letters?

    For clarity, SMI is sum -p log p.

    Because the distribution is uniform, the SMI of this distribution is log 26 per character. SMI is additive, so 2 characters have 2 log 26 SMI, 3 characters have 3 log 26 SMI, and so on.

    So, any N character word has SMI of N log 26 using this distribution.

    How is this as a starting point?

  48. 48
    gpuccio says:

    Nonlin.org:

    As you know, I will not enter a discussion with you. Just a question.

    Why should information not be quantifiable?

    Because it is an abstract concept?

    Does that mean that we cannot compute the figures of pi? Or measure speed?

    Just to know.

  49. 49
    EricMH says:

    Here’s an example of the discrepancy I note between what experts claim about Dembski’s theory, and what I’ve actually found in my research.

    http://www.sciencemeetsreligio.....theory.php

    > Indeed, there is no “conservation” law with respect to any of the most widely employed measures of information (Shannon, Kolmogorov or Chaitin) employed in information theory research.
    > …
    > Dembski’s central argument, namely that there is a “Law of Conservation of Information” that rules out natural evolution of highly complex biological structures, is without foundation.

    This is false. There are at least two conservation laws in Shannon and Kolmogorov-Solomonoff-Chaitin information theory.

    1. For Shannon mutual information there is the data processing inequality.
    2. For Kolmogorov-Solomonoff-Chaitin algorithmic mutual information there is Leonid Levin’s law of information non-growth.

    Dembski’s CSI is a form of mutual information, and consequently the two laws above apply. Levin’s law is the strongest and proves that no combination of deterministic and random processing can increase mutual information, which would mean natural processes cannot increase CSI, as Dembski also argues.

    Why do experts in the field make incorrect criticisms like this? One possibility is Levin wrote in Russian, and his work may not have been translated when the critics were learning information theory. Perhaps the data processing inequality is also a new development. At any rate, the experts should update their criticism.

  50. 50
    Nonlin.org says:

    gpuccio,

    Good questions.
    It’s not about what “should be” but about “what is”.

    Yes, information is not quantifiable because it is abstract and user dependent. Example: ‘circle’ vs ‘square’. Example: ‘mother’ may mean nothing to you, and may be a partial answer to his “what risk factors?”

    Pi is not information, but a fact of life. Information resolves uncertainties that only organisms can have. Someone created information by observing the fixed ratio in a circle, so all you need is circumference of A and B and diameter of A to find diameter of B (no Pi needed). Then Archimedes created more information – the algorithm for calculating Pi. We still don’t know and don’t need Pi, but a good enough approximation. ‘Speed’ and anything else also starts with an intelligent agent asking a question and same/another resolving that uncertainty by creating information.

    EricMH,

    Thanks for acknowledging. The intent is not to put anyone on the spot but to speed up progress in resolving once and for all Intelligent Design vs Darwinist Evolution by eliminating bad arguments.

  51. 51
    EricMH says:

    @Nonlin.org could you explain how your terminology clarifies the question of meaning in data?

    How would you quantitatively distinguish between these two strings, one gibberish and one meaningful?

    1. xefiytgvkcjmsqgrnrjc
    2. antiauthoritarianism

    The ID way using a uniform chance hypothesis (CH) and the 2nd Edition Webster dictionary for specification (S), which has 218,632 words. The dictionary is a detachable specification because it does not change the probability of generating a specific sequence from the uniform distribution. Thus, for an event (E), P(E|CH,S) = P(E|CH).

    The complexity term for both is 20 * log2 26.

    The specification term for #1 is also 20 * log2 26, since the context provides no help in describing it.

    The specification term for #2 is log2 218,632, since we can describe it by indexing one of the words in the dictionary.

    So, CSI for each entry is:
    1. 20 * log2 26 – 20 * log2 26 = 0
    2. 20 * log2 26 – log2 218,632 = 338

    In the first case we cannot eliminate the chance hypothesis, but in the second case we can.

    Note that in case #2 we can only say intelligent agency is responsible if the uniform hypothesis adequately describes the available chance mechanisms.

  52. 52
    Nonlin.org says:

    EricMH,

    You cannot distinguish between the two except from context. Information is always encoded and maybe encrypted. The first can be an encrypted message and second can be a random sequence in a very long white noise sequence.

    Deciphering key is essential. Remember the Enigma machine. Turing KNEW the data was not random and reverse-engineered the key.

    To detect Intelligent Design, we need to reject the ‘Random’ null hypothesis FIRST. This is standard practice:

    If we search for extraterrestrial life, archeological artefacts, geologic events, organic traces, etc., we infer presence based on specific nonrandom patterns. Typical threshold (p-value) is 0.05 meaning “if the outcome were due to randomness (null), it would only be observed in 5% or less of trials”. To reject the “randomness” hypothesis, the actual threshold is not critical, as probabilities get extreme quickly. For instance, given a 10 coin toss set, the probability of that set matching a predetermined sequence (this could be the first set sampled) given a fair coin is 0.1%, well below the 5% threshold. A quick glance at biological systems show extreme precision repeated over and over again and indicating essentially zero probability of system-level randomness. Kidneys and all other organs are not random, reproduction is not random, cell structure is not random, behavior is not random, etc.

    http://nonlin.org/intelligent-design/

    …luckily, natural data is not encrypted.

  53. 53
    EricMH says:

    @Nonlin.org couldn’t biological systems just be the equivalent of a random sequence in a very long white noise sequence?

  54. 54
    Mung says:

    EricMH

    At any rate, the experts should update their criticism.

    🙂

  55. 55
    gpuccio says:

    Nonlin.org:

    Only one comment: you are really good at generating nonsense.

    Please, take it as a compliment! 🙂

  56. 56
    EricMH says:

    @gpuccio, Nonlin.org’s comment seems pretty coherent to me, although one might disagree with his conclusion. What is nonsensical about it?

  57. 57
    EricMH says:

    @Mung, according to the article author the two conservation laws I list are quite different from what Dembski was trying to do. Unclear why that is the case, but that’s the current expert response…I’m asking whether he can elaborate on why they are different.

    I don’t understand, since I can manipulate Levin’s proof to apply to CSI.

  58. 58
    EricMH says:

    To elaborate on my last point, here is what Levin proves in his paper, where I(X:Y) is the algorithmic mutual information between X and Y:

    E[I(X,Z:Y)] <= I(X:Y).

    This inequality can be rearranged into the following, where I(Z) is -log2 P(Z):

    E[I(Z) – K(Z|Y)] <= 0.

    And the definition of CSI is Dr. Ewert’s ASC version:

    ASC(Z,Y,P) = I(Z) – K(Z|Y).

    So, we get:

    E[ASC(Z,Y,P)] <= 0

    Therefore, we can see Levin's proof applies to Dembski's CSI and there is an applicable law of information conservation in standard information theory. Thus, experts are behind the times (Levin’s proof came out in 1974) and need to update their criticism of Dembski.

  59. 59
    Nonlin.org says:

    EricMH @53

    Theoretically, on an infinite scale anything is possible, even a Boltzmann brain. Darwinists also claim that Infinite Monkeys could create Hamlet or The Odyssey.

    But this is not what we observe in nature:
    1. The meaningful random strings produced experimentally are shorter than imagined.
    2. Random-generated meaningful strings are preceded and followed by gibberish
    3. WE, the intelligent users, give meaning to those strings.
    4. Hamlet was followed by King Lear, Macbeth, etc as well as countless authors inspired by Shakespeare. And he took inspiration from others in an endless meaningful series.
    http://nonlin.org/random-abuse/

    Same goes for life. It’s not just that your kidneys are amazing machines, but also that everyone has amazing kidneys including cats, dogs, and chickens.

    Re “antiauthoritarianism”, who cares? ID is not trying to solve that particular mystery, so we can afford a very generous threshold (to identify Design) and a very wide “I don’t know” gray zone. When it comes to life, the smarter Darwinists understand they have a “randomness” problem so they try and fail to sneak in order via the magic of “natural selection”.

  60. 60
    EricMH says:

    @Nonlin.org all I’m saying is your random sequence criticism seems to apply just as much to the argument you propose, since any possible observation we can refer to is finite. So, I’m having trouble distinguishing between your argument and mine. Perhaps there is no difference and we are saying the same thing, just in different ways.

    What is your solution to the problem of infinite probabilistic resources?

  61. 61
    Nonlin.org says:

    EricMH,

    Not sure we’re saying the same thing as I don’t see the need for your “specification”, and gpuccio’s “function”.

    Much simpler than that: the hallmark of design is ‘order’. This need not be specified or functional. Yes, the bowling ball is simple but designed. And so is cubist art. Let’s start from there.

    No need to discriminate against crystals gravity and all those laws and particles out there – the best inference is that they are designed as well: http://nonlin.org/intelligent-design/

    We can all agree on measuring complexity, but in your example @51 you refer to Webster’s for “specification”. Who provides a dictionary for nature? Also, art clearly violates gpuccio’s “function” requirement and we had an extensive discussion about that.

    What do you mean “the problem of infinite probabilistic resources”? All inferences are statistical. And the search space is limited. Who cares that the human genome is seen in some obscure galaxy radiation? We see it in every human cell, so the search space is much smaller, hence pattern is much less likely to be random. And again, probabilities get extreme very quickly.

  62. 62
    EricMH says:

    @Nonlin.org, it sounds like you are also using a specification with your concept of ‘order.’ If you were to mathematically define order, you’d probably end up with something similar to Kolmogorov complexity.

    The problem of infinite resources is what you said before:
    > second can be a random sequence in a very long white noise sequence.

    All your pieces of ID evidence are finite, so could be a random sequence in an infinite white noise sequence, since all finite sequences show up in an infinite random sequence. What is the difference between your pieces of evidence and my #2 such that the former are evidence of ID and the latter is not? Both are finite, so it seems the infinite random sequence objection applies equally to both.

  63. 63
    gpuccio says:

    EricMH at #56:

    I was referring to comment #50, which is, IMO, utter nonsense.

    Do you agree with the things he says there? Just to know.

  64. 64
    EricMH says:

    @gpuccio, I agree with parts and disagree with parts, but I would not consider it nonsense. Nonlin.org makes coherent claims. Offhanded dismissal is what the other side does. I don’t want to repeat it on our side.

  65. 65
    Nonlin.org says:

    EricMH,

    I am trying to improve on Dembski’s filter, so yes, there is a connection. However the approach is different and mine improves in several areas:
    – only two decision blocks as opposed to three
    – other than equating Design with Necessity, nothing in the diagram should be controversial to anyone
    – no need for any predetermined threshold – one can always allow for x% chance the outcome occurred randomly (accommodates the infinite resources problem)
    – not dependent on clear definition of ‘contingent’, ‘specified’, ‘complex’. What do those mean anyway and how does one select those thresholds? Yes, I read about them, but they’re still iffy to me and likely many others, and that’s a problem.
    – ‘order’ is simply an outcome of rejecting the Null hypothesis. No need for Kolmogorov complexity.

    I welcome any feedback, so feel free to criticize my filter.

  66. 66
    Nonlin.org says:

    gpuccio,

    Why don’t you take apart what what I said an clarify your disagreement? Maybe I can explain some parts, and maybe you’re right about others. It’s impossible to disagree with everything and not be able to express it.

  67. 67
    PaoloV says:

    By information do you mean this or this?

    By biological information do you mean this or this?

  68. 68
  69. 69
    EricMH says:

    @Nonlin.org, I agree your approach is simpler. I’d like to understand better how you eliminate the infinite resources problem. You say everything reduces to the singularity, so couldn’t there have been an infinite number of big bangs, and we just got a lucky one? No need to invoke intelligent design. So, I don’t really see how your explanatory filter actually can indicate intelligent design. It would not even do so in the case of human designers, since they just reduce to a lucky big bang, so are no more special than flipping a fair coin enough times.

    @Paolov by information I refer to Dembski’s concept of complex specified information (CSI). It is a variant of mutual information in both Shannon and Kolmogorov information theory, with the added condition of an independent target variable. From what I’ve seen of functional information, it would be described by CSI. I’ll have to dig into the topic more deeply, however.

  70. 70
    EricMH says:

    @Nonlin.org for the record, I don’t believe ID has a ready answer for the infinite resources problem, either. Or, at least I have not heard of a principled reason. So at that point it would reduce to faith whether one wants to believe in infinite chaos or a designer. The problem is the former is well defined and the latter is not.

  71. 71
    PaoloV says:

    EricMH @69:

    Thanks for the at least partial clarification.

    Please, keep in mind that I consider myself among the most ignorant folks in these discussed topics. However, I want to learn as much as I’m allowed to.

    I think information is generally well defined in the links given @67. We don’t need another general definition, do we?

    I think Complex Specified Information is a very important category of information, it’s a subset of the general definition.

    If we add the “functional” attribute, then we move to yet another category (or maybe subcategory?) of the general concept of information given @67.

    The same approach can be taken to describe and understand biological information. The qualifier “biological” must be taken into account.

    Perhaps this is one of the reasons why it’s so difficult to discuss this topic: lack of agreement on the exact definition we’re basing our discussion on. Maybe that’s one reason why it seems like we’re talking past each other.

    However, the main reason we humans have difficulties discussing important issues is that good communication is not an attribute we humans are naturally endowed with.

    Let’s just look around everywhere we are and we’ll see it right there. But mainly, let’s look at ourselves with critical eyes and it will be obvious that we’re not good communicators.

    We talk quite authoritatively about things we don’t know well. We don’t like to ask questions in order to learn and understand. We don’t like when others ask questions that require us to explain in details what we understand about any given issue, maybe because it could expose our lack of understanding?

    This communication problem seems to indicate our general lack of humility to admit our deficient knowledge.

    Ok, enough cheap philosophizing! 🙂

    Let’s go back to some interesting issues you touched @ both 69 and 70.

    Let’s assume we’re in one of an infinite number of universes, which happened to have the physical parameters scientists observe and measure.

    However, let’s assume that this particular universe we are in somehow had its beginning certain time ago. Let’s denote that elapsed time “Tu”.

    Apparently you and I, as well as the rest of the discussants in this thread and maybe even in this website, are in this same planet we call Earth. Let’s assume for the sake of simplicity that this particular planet we are temporarily occupying these days originated somehow certain time ago. Let’s denote that elapsed time “Te”.

    By the way, as a brief digression, let me say that someone I know speaks a language where “Tu” means “you” and “Te” is kind of like a reflexive “yourself” or something like that. Therefore, for him the combination “Tu Te” is very common in conversation in his language.

    But let’s get serious here.

    No matter how our universe could have popped up, it seems like our planet has been around this time “Te”, which is infinitely smaller than infinite.

    Therefore, when the discussion gets into this information “concoction” with the intriguing attributes “biological”, “complex”, “specified” and “functional” all mixed in a wonderful -but still poorly understood- “blender”, our explanations, in order to be taken seriously, must be carefully expressed in simple terms, but highly comprehensive and with maximum coherence.

    I think that gpuccio refers to “Te” when he presents his elaborate explanations on the above-mentioned information “concoction” relative specifically to protein families. I don’t think gpuccio’s explanations depend much on “Tu” (if at all), but does he care about anything before the start of “Tu”? Well, these are questions for gpuccio.

  72. 72
    gpuccio says:

    EricMH:

    I agree with parts and disagree with parts, but I would not consider it nonsense. Nonlin.org makes coherent claims. Offhanded dismissal is what the other side does. I don’t want to repeat it on our side.

    Of course you don’t know the background, so I can understand that you write what you write.

    But the simnple truth is: my dismissal of Nonlin.org’s ideas may be right or wrong, but certainly it is not “offhand”.

    It is, indeed, deeply motivated.

    You see, Nonlin.org and I share a long past history of discussion.

    You can look, for example, at the thread in my OP:

    Defending Intelligent Design theory: Why targets are real targets, probabilities real probabilities, and the Texas Sharp Shooter fallacy does not apply at all.

    https://uncommondescent.com/intelligent-design/defending-intelligent-design-theory-why-targets-are-real-targets-propabilities-real-probabilities-and-the-texas-sharp-shooter-fallacy-does-not-apply-at-all/

    where the discussion starts with a comment by Nonlin.org (comment #1), and “ends” with a comment by Nonlin.org (comment #489). If you have the time and the patience, you will find there a long and detailed confrontation between him and me, always rather respectful, where we have really dealt in great detail with a lot of aspects of what he thinks and of what I think.

    I will just quote her a coup’le of my final comments, just to explain why I dismiss his arguments:

    My comment #463:

    “I don’t wnat to go on infinitely with you. I will try to address a few more points, but please, let’s stop at some level!”

    My comment #468:

    “I am not frustrated, but I will not follow you along these lines of reasoning. I apologize in advance, but I really believe that what you say has no sense, and I have not further time to waste.

    Nothing personal, believe me. You have all my goodwill and, if you want, friendship. But enough is enough.”

    In brief, I have nothing against Nonlin.orf as a person. He is a nice guy, he is available to discuss, he is respectful. He is certainly in good faith. And he is certainly very creative.

    Unfortunately, I have cone to the stronly motivated conclusion, after wasting hours and hours trying to debate with him, that he is obsessed with a few weird ideas, that he believes to be absolutely true.

    Nothing bad in that, each of us is, in some measure, obsessed with his own ideas.

    But, ufortunately, I have come to the strongly motivated conclusion (right or wrong that it may be) that his ideas have nothing to do with science, or with good, or even acceptable, philosophy.

    They are bad philosophy, and nothing more.

    I am not happy to say that, but it’s exactly what I believe.

    It’s not even a question of some things being right, and others wrong. He is a very consistent and very obstinate thinker. As most of his fundamental ideas are wrong, even the right parts are wrons, if you understand what I mean.

    If uou want, you can try to understand better his general worldview by reading his essays at his site:

    http://nonlin.org/

    I must say that I have rarely seen a site where someone says so many right things for the wrong reasons.

    For me, this is really disturbing. That’s why, seeing that even long and detailed discussions could not bring us anywhere nearer, I have decoided not to have discussions with him.

    Indeed, my comment #48 here, addressed to him, starts with the following statement:

    “As you know, I will not enter a discussion with you. Just a question.”

    But it seems that even a question was too much.

    That said, if you want to know some of his statements that, IMO, are utter nonsense, just from the few things he has posted here, her is a list:

    “BTW, I also disagree with Robert Marks’ claim that a picture of Mt. Rushmore contains more information than one of Mt. Fuji. That’s because information is abstract and user dependent. Does a circle have more, less, or same information as a square?” Comment #9

    “information is not quantifiable (only data is) and design must be inferred from regularity, not information (see art)” Comment #46 (this is the one that triggered my question)

    The, form the “precious” comment #50:

    “Yes, information is not quantifiable because it is abstract and user dependent. Example: ‘circle’ vs ‘square’. Example: ‘mother’ may mean nothing to you, and may be a partial answer to his “what risk factors?””

    “Pi is not information, but a fact of life.”

    “Someone created information by observing the fixed ratio in a circle, so all you need is circumference of A and B and diameter of A to find diameter of B (no Pi needed). ”

    “We still don’t know and don’t need Pi, but a good enough approximation. ”

    “‘Speed’ and anything else also starts with an intelligent agent asking a question and same/another resolving that uncertainty by creating information.”

    And still:

    “Information is always encoded and maybe encrypted.” Comment #52.

    “Not sure we’re saying the same thing as I don’t see the need for your “specification”, and gpuccio’s “function”.” Comment #61. well, as for me, I have no doubts: we are not saying the same thing. As for you (Eric), you decide.

    “Much simpler than that: the hallmark of design is ‘order’.” Comment #61.

    “No need to discriminate against crystals gravity and all those laws and particles out there – the best inference is that they are designed as well” Comment #61

    “Also, art clearly violates gpuccio’s “function” requirement and we had an extensive discussion about that.” Comment #61. Maybe we had, among many others, but it is nonsense just the same.

    Well, the list is already long enough.

  73. 73
    gpuccio says:

    PaoloV:

    Of course I like your questions! 🙂

    Some clarifications.

    I like explicit definitions. That’s why I have started my OPs here, long time ago, by giving explicit definitions of “design”, “functional information” and “complex functional information”.

    Those definitions are in perfect accord, IMO, with Dembski’s original and basic ideas, but they certainly are not based on his later paper about specification, that I have never fully understood, or simply agreed with.

    As I have said many times, my approach is purely empirical. I am not a mathematician.

    I do believe that the whole problem of specified information in biological objects can and should be addressed using the empirical concept of functional information.

    I do believe that function should be kept separate from order. Which is one of the things that Nonlin.org seems to be completely confused about.

    I do believe that any discussion about biological information must consider a specific empirical setting: our planet, its resources, its life span. That’s the scenario where biological information arises. That’s what has to be explained.

    However, the levels of functional complexity observed in most individual biological objects are so huge that even the life span of the whole universe makes no real difference: after all, the difference is less than one order of magnitude.

    I am definitely not interested in any discussion about the multiverse in relation to biological informtion. That’s simply no science.

  74. 74
    Bob O'H says:

    EricMH @ 47 –

    The key to avoid the dilemma you present is the specification must be independent of the event.

    But how can you do that if you have several possible specifications and you take the maximum? That automatically makes it data dependent. You can only have a specification that is independent of the data if you only have a single specification, but then I don’t know how you get this objectively. Come to that, I don’t know how you ensure that this is “the” CSI that is the objective property of an object.

  75. 75
    Mung says:

    PaoloV:

    By information do you mean this or this?
    By biological information do you mean this or this?

    Excellent questions!

    The first thing to do in a discussion of this sort is to separate the concept of information from the concept of a measure of information.

    Shannon Information is a misnomer as what Shannon provided were information measures.

    Complex Specified Information is also a misnomer as it is likewise a measure.

    And the exact same thing can be said of Functional Information.

    They all provide us with quantities or amounts.

    Now let’s see if we can get everyone to agree that what are are talking about are measures.

    This is why I like to use the term SMI, for Shannon’s Measure of Information, following Arieh Ben-Naim.

  76. 76
    gpuccio says:

    Mung:

    I am not sure I understand what you mean.

    A measure is a numerical assessment relative to some physical quantity. A measure is made of a number and an unit of measure, but oit refers to some well defined physical quantity (or property).

    So, 13 metyers is a measure of length. 5 grams is a measure of weight.

    You have to clearly define the quantity (or property) to make sense of the measure.

    So, functional information is the quantity or property, and individual measures are measures of it.

    Why do you emphasize the measure over the defined physical quantity (or property)?

  77. 77
    Mung says:

    EricMH:

    @Mung, I apologize for lack of precision. How about we start with a uniform distribution over the 26 English letters?

    For clarity, SMI is sum -p log p.

    Because the distribution is uniform, the SMI of this distribution is log 26 per character. SMI is additive, so 2 characters have 2 log 26 SMI, 3 characters have 3 log 26 SMI, and so on.

    So, any N character word has SMI of N log 26 using this distribution.

    How is this as a starting point?

    I think we agree, though you haven’t provided actual numbers.

    If our alphabet has only two characters, say 0 and 1, and the probability distribution is uniform, then SMI gives us 1 bit. Example, tossing a fair coin. You would only need to ask a single yes/no question in order to know whether the outcome of a coin toss was heads or tails.

    D:\projects\information_theory>ruby -e “puts [0.5,0.5].inject(0) {|sum, px| sum + px * Math.log2(1.0/px)}”
    1.0

    Double the number of characters to four and the “entropy” doubles. We have twice as many possible outcomes where each outcome is equally probable. Example a four sided die.

    D:\projects\information_theory>ruby -e “puts [0.25,0.25,0.25,0.25].inject(0) {|sum, px| sum + px * Math.log2(1.0/px)}”
    2.0

    It takes two yes/no questions (only one more than before) to ascertain or “specify” the outcome even though the number of possible outcomes has doubled.

    Eight equally probably outcomes, the possibilities have doubled again, but only one more yes/no question is needed:

    D:\projects\information_theory>ruby -e “pr = 1.0/8; puts [pr,pr,pr,pr,pr,pr,pr,pr].inject(0) {|sum, px| sum + px * Math.log2(1.0/px)}”
    3.0

    What about a six sided die?

    D:\projects\information_theory>ruby -e “pr = 1.0/6; puts [pr,pr,pr,pr,pr,pr].inject(0) {|sum, px| sum + px * Math.log2(1.0/px)}.round(2)”
    2.58

    Here it’s easier to see that we are dealing with an average quantity.

    Now the neat thing is that this does tell us something about encoding and upper bounds. But that’s for a separate post. But the point is that this can be done for any probability distribution and that Shannon’s measure is over a probability distribution.

    I don’t think we disagree about this. But i think it is important the people understand that it is a measure and just what it is that the measure applies to. And we can do this without any talk of messages or communication or encoding or “information content” (or even entropy).

    And of course it still works even for non-uniform distributions.

    Oh, but back to a 26 character alphabet where each outcome is equally likely, again a uniform distribution:

    D:\projects\information_theory>ruby -e “dist = Array.new(26) {1.0/26}; puts dist.inject(0) {|sum, px| sum + px * Math.log2(1.0/px)}.round(2)”
    4.7

    Is that the same answer you got?

  78. 78
    Mung says:

    Hi gpuccio!

    A measure is a numerical assessment relative to some physical quantity. A measure is made of a number and an unit of measure, but oit refers to some well defined physical quantity (or property).

    I agree about the number and unit. For what we are talking about the standard unit is the bit, but it does not have to be that.

    https://en.wikipedia.org/wiki/Nat_(unit)

    Now, do you consider a probability distribution to be “some well defined physical quantity (or property)”?

    The main point is that we are talking about probability distributions. Isn’t it true that FI is a measure given a probability distribution?

    Can you calculate FI without one?

  79. 79
    gpuccio says:

    Mung:

    A probability distribution is a mathematical object by which we try to describe, as well as possible, some physical system.

    Functional information (in bits) is defined as -log2 of the ratio between the numerosity of the target space and the numerosity of the search space, and in that definition we assume a probability distribution which is more or less uniform.

    In the end, functional information is -log2 of the probability to find the target space in a well defined system.

    The system we are referring to is some physical system where, by some modification, a new configuration can arise in an object. That configuration can be part of the target space, or not. The probability that a new configuration may be part of the target space is what we are considering. -log p of that probability is the functional information linked to that function, as defined, in that system.

    So, each value of FI is a measure, but the concept of FI is a property (defined for a function in a system).

    I think that, if we keep our concepts well defined and separated, everything is rather clear.

  80. 80
    EugeneS says:

    GP,

    I must say I agree with your opinion about what Nonlin writes, which I find is somewhat strange. From time to time you get interlocutors like him. In my Russian blog, I have a friend that also denies natural selection as non-existent. He claims that it is not possible to measure fitness in practice because the size of the population depends on many things including random factors. There is of course some truth to it but I cannot get rid of the impression that this is all just untidy reasoning.

  81. 81
    DATCG says:

    Nice conversation.

    Nonlin,

    Curious, have you read Trevor and Abel’s paper on Three Subsets of Random, Ordered and Functional Sequences?

    If you’ve not read it, here it is…

    Three Subsets of Sequence Complexity and their relevance to Biopolymeric Information

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1208958/

    They draw a line between Order Sequence and Functional Sequence. And I think they make a good explanation as to why the difference matters for us 🙂 Living beings.

  82. 82
    EricMH says:

    @Mung, yep tracking with you.

    >>> from math import log
    >>> round(reduce(lambda a, b: a – b*log(b,2),[1/float(26)]*26,0),2)
    4.7

    I agree we are talking about a measure called SMI. What does it measure?

  83. 83
    gpuccio says:

    EugeneS:

    Hi! 🙂

    “Untidy reasoning” is a very good way to put it.

  84. 84
    PeterA says:

    Glad to see the always serious and interesting comments by EugeneS and DATCG again! I enjoy them, specially in the same discussion thread with gpuccio.

  85. 85
    Nonlin.org says:

    PaoloV @67

    Too many definitions out there. Information is the entity that resolves an uncertainty. Note that only intelligent agents can have uncertainties and only intelligent agents resolve these uncertainties.

    Anything that mentions ‘message’ or ‘data’ is NOT information as these may or may not carry information. ‘Entropy’ applies to data, not information. Both of your long sources are wrong repeatedly.

  86. 86
    Nonlin.org says:

    EricMH @69,

    I do not say “everything reduces to the singularity”

    I use Pro/Con notes and that’s a “Con” from an AMAT. I disagree with that and answer under “Pro”: “How can a point of disruption where all our knowledge completely breaks down explain anything? To the best of our knowledge, Intelligent Design is responsible for that singularity and more.”

    EricMH @70

    I explained “infinite chaos” doesn’t make any sense. Even AMATs reject that. Here’s one more: if all were due to infinite chaos, how come you reply to my comments and I to yours? Since our actions are (don’t seem) random now, it means there’s a long chain of actions and reactions. I can’t believe some people oscillate between “infinite chaos” and “complete determinism”. Anything but common sense…

  87. 87
    Nonlin.org says:

    gpuccio @72,

    Don’t be bitter. Yes, those are my comments and I stand by them. Now, do you want to challenge any of them?

    How am I confused about “function should be kept separate from order” when it comes to design? Are you denying that function-less art is in fact designed? This is too elementary.

  88. 88
    Nonlin.org says:

    EugeneS @80

    So you agree your friend is right, yet it’s “all just untidy reasoning”? Wow!

    Did you see that “fitness” is only one of many reasons why “natural selection” is impossible? Feel free to share with your friend:
    http://nonlin.org/natural-selection/

  89. 89
    Nonlin.org says:

    DATCG @81

    Interesting. However, the task at hand is identifying design. Some design is functional with at least partially known function, some may be functional but with unknown function, and some is not functional (art). Whoever tries to limit the search to known function, misses a lot of designs.

  90. 90
    EricMH says:

    @Nonlin.org not sure AMATs reject infinite chaos. Seems to be the same thing as infinite universes. But, at any rate, I think the main difference between your viewpoint and ID is you say necessity and design are the same thing, whereas ID states design is a third causal category that can be distinguished from necessity. I would say your viewpoint is closer to neo-Platonism or Spinoza’s philosophy than ID. The former suffer from a problem of justifying the a priori necessary information that produces everything else. In the end, my intuition is they have the same kind of overfitting problem as AMAT, although their problem is fitting an overly complex deterministic function whereas the AMAT problem is they fit noise. I believe intelligent causation is a necessary component of a scientific framework that doesn’t overfit the data.

  91. 91
    gpuccio says:

    Nonlin.org:

    I still don’t want to discuss with you again.

    Just a list of suggestions:

    1) Try to understand the difference between descriptive information and prescriptive information, as clearly discussed by Abel, and how both are designed (if complex).

    2) Note that only intelligent agents do science.

    3) You are very confused about order. I cannot even understand what you mean with that word. Maybe you could try to offer explicit definitions, instead of vague and conflicting “ideas”.

    4) I am not bitter. Just tired of having to do with you.

    5) Design has always a purpose. That purpose can be to do something by the designed object. In that case we speak of prescriptive information, and of function, That’s what we observe in biological objects.

    Of course, design can also generate descriptive information: a book, a poem, a painting. The purpose here is to express conscious experiences and to evoke similar experiences in others. Or just to convey meaning.

    We use function definition to detect prescriptive information. The problem is not that we miss a lot of designs. As I have explained many times, the purpose of detecting design in biological objects is not to have high sensitivity, but absolute specificity.

    In case you are interested in real science, the tradeoff between sensitivity and specificity is one of the main points in understanding empirical science. Have a look at that.

    However, we can define “functions” for descriptive information too. Not in terms of “doing something” with the object, but rather in terms of “conveying some experiences or meanings” by the object. That approach can be used to measure functional information, too.

    For example, a piece of text can convey specific meanings, or not. I have used that kind of definition in my OPs about English language. But that approach is not specially useful with biological objects, that carry mainly prescriptive information.

    OK, that’s already too much discussion for now.

  92. 92
    EricMH says:

    @Bob O’H, in the case of selecting from multiple specifications, we have to make choosing the specification part of the description length. For instance, if we have 8 possible specifications then we add log2 8 = 3 bits to the description, because we’ll need 3 bits to pick one of the specifications.

  93. 93
    Bob O'H says:

    Oh, I hadn’t seen that part of the specification. But I don’t get the point – you will (presumably) add log2 8 bits to every specification, so you still end up with the same ranking. The absolute value will change, so “the” value of CSI is subjective in that it now depends on the number of specifications.

    All of this still deosn’t get around the problem that if you take the maximum of the specifications, the specification isn’t independent of the data.

  94. 94
    EricMH says:

    @Bob O’H, those are good points.

    Picking from the subset doesn’t make the empirical measurement completely objective, but gets closer to the objective value.

    Using log2 N introduces a penalty for the reduction of independence you noted.

    There are two questions getting combined in your responses. One question is whether there is such a thing as objective CSI. Another question is how our subjectively derived specifications (from Bill and Bob) approximate the objective value. My answers are dealing with the latter scenario you proposed.

  95. 95
    EricMH says:

    @Bob O’H, here’s another take on your objection. There are an infinite number of possible specifications, so the log2 N approach always gives everything an infinite specification, making all events have negative CSI.

    So, we need a way of indexing specifications that doesn’t require an infinitely long number. One way is to index each specification by its optimal compression, K(S), so every specification has a finite index.

    In this way, the CSI for an event is calculated as -log2 P(X) – K(X|S) – K(S), which is the same as -log2 P(X) – K(X,S).

    Let’s call this objective CSI (oCSI):

    oCSI(X,S,P) = -log2 P(X) – K(X,S).

    Thus, the objective CSI is found by minimizing oCSI(X,S,P) over all possible S, where the dependence penalty is K(S).

  96. 96
    Mung says:

    gpuccio:

    I think that, if we keep our concepts well defined and separated, everything is rather clear.

    That is exactly what I am trying to encourage!

    🙂

  97. 97
    Mung says:

    EricMH:

    I agree we are talking about a measure called SMI. What does it measure?

    That is the question!

    Is it measuring information and in what sense does it quantify “an amount of information.”

    But first, whatever it is measuring, it has to do with the probability distribution. To lose sight of that makes it easier to go astray.

    Does it measure “information” or “information content”? If it does, it is measuring the information or information content associated with a probability distribution.

    If you have two distributions that are the same you will get the same quantity regardless of “message content.”

    As to what it measures, there are a variety of interpretations about that. Are some interpretations better than others? Are some interpretations of “entropy” better than others?

    I believe so, but that can wait for a future post.

    Choice, uncertainly, surprisal, information …

    entropy = all the above? LoL.

  98. 98
    EricMH says:

    @Mung, did you determine if entropy = disorder?

  99. 99
    Bob O'H says:

    Eric @ 95 – so -CSI is now the sum of Shannon and Kolmonogorov? And there is no log N? And how does this reduce the dependence from taking the maximum?

    I’m now utterly lost trying to understand what’s going on. I suspect I’m not the only one.

  100. 100
    EricMH says:

    @Bob O’H, CSI hasn’t changed dramatically, I just added another term for the specification. The rest is the same. The dependency issue is taken care of by establishing a penalty for dependency, which is the size of the specification.

    I had to add the dependency penalty because currently there is no well established approach to quantifying how independent a specification is. In the objective case we have to consider all possible specifications, because they are no longer limited by what humans can dream up.

    In the subjective case, independence was a heuristic. We just assumed descriptive language of some unrelated phenomena, such as human designed artifacts, were independent of biological phenomena that we’d never discovered before. Seems reasonable enough. But it isn’t a quantitative heuristic. I just made specification dependence quantitative so we can talk about the objective CSI that is independent of observers.

    Addressing the math. Since we’re minimizing over all S, we can remove the S from oCSI, giving just oCSI(X,P).

    What we want is to guarantee E[oCSI(X,P)] <= 0, so that give enough measurements we can definitively eliminate P as a valid source of X, and that criterion is met by oCSI.

  101. 101
    Nonlin.org says:

    EricMH @90

    I didn’t say “all amats”. Just “many”.

    If ‘necessity’ is not produced by the same Designer, then what’s the source of that ‘necessity’?

    I am definitely not a fan of Spinoza. You’re misreading.

    Not sure what “fitting”/”overfitting” means. Also not sure who believes “infinite chaos”. Ask any amat and they would say “natural selection” is not random.

  102. 102
    EricMH says:

    @Nonlin.org, sorry for the misunderstanding. We can get regularity from a Turing machine, which is a generalization of all finite mechanical processes. An extremely long string of 1s has a very short program, so is very likely. No designer required, if we grant the AMATs a Turing machine. Of course, why grant AMATs anything, including randomness? Nothing comes from nothing, and randomness is something.

    However, we are working within the context of modern science, which already grants randomness and Turing machines. So, we have to have some third causal source besides randomness and Turing machines if we want to say ID has something to offer modern science.

  103. 103
    Nonlin.org says:

    gpuccio @91,

    If you don’t wan’t to discuss, don’t 🙂 But I will reply to your comments and will comment on your views anyway.

    There’s a clear definition of order: “the arrangement or disposition of people or things in relation to each other according to a particular sequence, pattern, or method”. No chance to get confused.

    I know “sensitivity and specificity”. Don’t worry.

    You’re just repeating your argument but not clarifying anything with “descriptive/prescriptive information”. Look at how little traction Dembski got, and look at the criticism against him:
    http://wasdarwinwrong.com/kortho44.htm

    …pretty much same as mine including “how can you accept ‘natural selection’ and ‘micro-evolution’, but not macro-evolution”? ‘Function, ‘contingent’, ‘specified’, ‘complex’ and their arbitrary thresholds are unnecessary complications – read again comment 65 to see how I improve on those…

    Sorry, I see your disagreements, but no solid counterarguments.

  104. 104
    Nonlin.org says:

    ErichMH,

    Big mistake granting this and that.

    You’re also granting “natural selection”, “micro-evolution” and “laws of nature”. Of course “random” is unknowable from the outcome and has been greatly abused by amats. And what is the origin of Turing machines if not design?

    If you don’t mind, I must insist with one question:
    “If ‘necessity’ is not produced by the same Designer, then what’s the source of that ‘necessity’?”

    …and one more new one:
    How come Evolution News returns nothing on “specified complexity”? Don’t they agree with Dembski?

  105. 105
    Silver Asiatic says:

    nonlin

    …pretty much same as mine including “how can you accept ‘natural selection’ and ‘micro-evolution’, but not macro-evolution”?

    Theoretically that would be consistent. If selection preserves small changes, then over time it should mean macro-evolution.

    But in this case, the empirical does not match the theory. Mutations do not have the innovative power or frequency and selection does not have the time needed to extrapolate from micro to macro levels.

    Science cannot explain why organisms withstand micro-evolutionary change but resist change of species. Adaptations fluctuate around a mean and organisms have something inbuilt in them that resists macro-changes and which preserves (heals, restores) them as a species.

    For Darwinism, species are always on their way to becoming something else and with mixed environments and non-directional development there’s no reason why they are separated by distinct features.

  106. 106
    EricMH says:

    @Nonlin.org

    The information theory aspect of ID is not highlighted as much for a variety of reasons. I think the main reason is math is not something a lot of people find easy to deal with. It’s easier to grasp specific tangible things, and it is hard to believe an abstract subject like mathematics could conclusively demonstrate anything in the physical world. There are also a lot of criticisms from professors like Shallit and Perakh, and without a solid grasp of Dembski’s math, it’s hard to know if their criticisms are correct or not.

    Regarding necessity and design, on a philosophical level the AMATs don’t really have much to stand on. As you point out, nothing can be granted, because nothing comes from nothing. So, I agree, necessity and order cannot come from anything other than an intelligent designer, because they are something.

  107. 107
    EugeneS says:

    Nonlin,

    “If ‘necessity’ is not produced by the same Designer, then what’s the source of that ‘necessity’?”

    Everything that had a beginning was designed. Full stop.

    However, there is the scientific method with its limitations of scope and its power of inference, intended for mundane pragmatic purposes.

    If you do not distinguish between order and function, you will not achieve much in this sense (hence my criticism of sloppy reasoning). I agree with you that everything, apart from God, is designed (if I understand you correctly), but in terms of making scientifically non-trivial claims, you need that distinction.

  108. 108
    Nonlin.org says:

    SA,

    “NS doesn’t do this or that” is much weaker argument than “there is no NS”. Why go half measure? I am with the amats on this.

    But let’s see what actually happens in nature. I conclude (with proofs) that they’re all illogical: NS, micro/macro-evolution, “random mutations”, “divergence of character”, “DNA is recipe”, etc.

  109. 109
    Nonlin.org says:

    EugeneS,

    Sorry, I don’t understand at all this insistence on “function”.

    If we search for extraterrestrial life, archeological artefacts, geologic events, organic traces, etc., we infer presence based on specific nonrandom patterns, NOT ON FUNCTION. This is real life science happening every day in different fields.

    I see gpuccio @91 tries hard to make “function” relevant, including forcing art into “function”, but he’s totally unconvincing.

    Meanwhile, I propose a Design detection process that should be crystal-clear and uncontroversial TO ALL except where I equate ‘necessity’ with ‘design’. What’s wrong with that proposal?

  110. 110

    There is so much wrong on this thread. It’s depressing.

  111. 111
    PaoloV says:

    UB,

    please, point to what is wrong, or at least to a sample.

    readers might learn a few things.

    thanks.

  112. 112
    gpuccio says:

    Upright BiPed:

    “It’s depressing.”

    Yes, it is.

  113. 113
    kairosfocus says:

    Folks, it may help some to understand that necessary entities are framework for any world to exist. For instance ponder that absent distinct identity, a world does not exist.By direct force of logic, we thus have A and ~A, therefore twoness. Thence immediately the panoply of numbers and the logic of structure and quantity that accompanies that, i.e. mathematics is part of the fabric of reality, at least in that core part that we ponder. This is then the deep foundation for the observations on how powerful mathematical reasoning is. And much more. KF

  114. 114
    kairosfocus says:

    PS, that is also connected to the point that if a world now is (manifestly!) then something always was. For, true nothing, non-being has no causal powers. At the heart of this is that necessary beings are eternal, without beginning or prior cause, they are framework to any world. Such thinking is unfamiliar to the scientific mindset and yet it is its underpinning, metaphysics sets the table of possible beings and how they ever could be ordered in a world. Science then operates on that table.

    PPS, we properly distinguish order which may have low information content [e.g. asasas . . .] from functionally coherent and complex integrated organisation which is inherently of high information content and has a lot of meaningful information in particular. (Ponder the previous sentence as a string example.) One may also distinguish randomness, such as gtiq3789jskvutftu[o . . . .

  115. 115
    EricMH says:

    @KF very interesting point on how mathematics comes from the law of identity and non contradiction. I will have to ponder this.

    For the thread in general, it is clear there are many different takes on how information theory applies to detecting design.

    The OP is Dembski’s law of information conservation is corroborated by mainstream information theory’s law of information non-growth, which proves natural processes cannot create CSI. So, despite the skeptical criticism, Dembski’s work is mathematically sound.

    It’s also common sense because math exerts no causal influence on the world, so the fact the world can be explained so well mathematically has no natural explanation, i.e. “The Unreasonable Effectiveness of Mathematics in the Natural Sciences”.

    https://www.dartmouth.edu/~matc/MathDrama/reading/Wigner.html

  116. 116
    daveS says:

    EricMH,

    What do you think of this (unoriginal) idea for testing whether CSI is useful for detecting design:

    1) Begin with an 800 x 600 array of pixels, all white. (Or another array size, if preferred).

    2) An experimenter sets some probability distribution on the power set of the set of pixels. The experimenter would also have to lay out how she is going to calculate Kolmogorov complexity of sets of pixels.

    3) Have someone else (the “subject”) choose a subset S of the pixels, either deliberately designed or not. These pixels are then turned black, creating a picture of sorts, which is submitted to the experimenter.

    4) The experimenter then calculates (or estimates) CSI(S) and uses this to decide whether S was deliberately designed. Repeat steps 3 and 4 until a sufficient number of trials have been performed.

    Do you think that is a valid way to, at least in principle, determine the efficacy of CSI?

  117. 117
    daveS says:

    PS to #116:

    A related question: Could a computer be programmed to detect design using the above process? In other words, is this a task that AI can perform?

  118. 118
    EricMH says:

    @daveS, yes, I think your experiment is a way to detect design. The rub is in your second question. If it can be detected by AI, then it might be optimized by AI, potentially removing the human from the loop. You’ll have to guarantee the picture generator has no knowledge of the AI picture grader, so the grader is an independent specification. If you can do this, then your AI grader will detect intelligent agency.

  119. 119
    Mung says:

    Upright BiPed:

    There is so much wrong on this thread. It’s depressing.

    Put on some blues!

  120. 120
    Mung says:

    EricMH:

    @Mung, did you determine if entropy = disorder?

    No. 🙂

    It would depend on what you mean by entropy and what you mean by disorder. If you are talking Shannon entropy and the “order” or “disorder” of a probability distribution I am still looking at that.

    Can we tell how ordered or how disordered a probability distribution is?

    Patrick decided to get back into it over at PS. He said I could learn some facts from an article about entropy. One of those facts seems to be that entropy is “missing information.”

    So entropy = information = missing information = disorder.

  121. 121
    EricMH says:

    @Mung, thanks, it is all very clear now: information = missing information.

    If order = information, then this also means order = disorder.

    I’m learning a lot from the PS information theory experts.

  122. 122
    Silver Asiatic says:

    Nonlin

    “NS doesn’t do this or that” is much weaker argument than “there is no NS”. Why go half measure? I am with the amats on this.

    I am open to what you have to say. There are many reasons why Darwinian explanations are illogical, as I see it. So, I wonder what is your proof that “there is no NS”.
    1. How do you define NS?
    2. How do you refute the existence of NS in the commonly cited examples that are given?

    In general, what is your basic argument?

  123. 123
    Silver Asiatic says:

    EricMH

    @KF very interesting point on how mathematics comes from the law of identity and non contradiction. I will have to ponder this.

    A thing is itself and not something else.
    There is one thing. There is another thing. Thus, two things.

  124. 124
    EugeneS says:

    Nonlin @104

    “What’s wrong with that proposal?”

    Because order is fundamentally NOT function.

    You will not be able to distinguish between ordered and functional patterns. And, consequently, you will not be able to infer ‘extra’ design intervention necessary to build complex function on top of already existing physicality (which we, ID supporters and opponents, agree to have by default).

  125. 125
    EricMH says:

    @EugeneS, seems order is related to function. Function is not disorderly, although it is also not simplistic order. I’d say the idea of function correlates well with compressible sequences that also have high Kolmogorov complexity. For example, a lengthy program has high Kolmogorov complexity, but there is also compressible structure to the code, hence why text compression algorithms work pretty well on source code.

  126. 126
    EugeneS says:

    Eric, Nonlin:

    This is order:

    https://goo.gl/TDRk6B

    and this is function:

    https://goo.gl/tNgX4Z

    Pretty different things.

    Code is not as compressible as regular strings.

  127. 127
    Axel says:

    @ the Mungster

    ‘Where can I get me a gizmeter? I assume it can measure anything at all? Can I replace my infometer with a gizmeter?’

    It can do just about anything, Mung. But there’s only one of them, and I possess it. However, I have found it prudent to be secretive about thinggies I invent and wish to patent, so I hope you will pardon the reticence I feel I must observe on the subject of my polyfunctional gizmeter. Thank you, in advance.

    Kindest regards
    Hugo Grimes, KFC, BSc, PhD, of this parish.

  128. 128
    EricMH says:

    @EugeneS sand dunes are functional? I thought function meant that the DNA gets turned into a protein that serves a particular purpose, and we are discussing whether there is a way to tell from the DNA format itself whether it turns into such a thing or not. Unclear how sand dunes apply to our discussion of function…

    As long as computer code is not encrypted, there are measurable differences.

    Now, if the code is encrypted/compressed, we can still tell from the broader context whether it is functional based on whether it does something or not, and whether removal of code breaks the functionality. However, we cannot say a particular section of code is non functional as easily.

  129. 129
    Mung says:

    EricMH:

    I’m learning a lot from the PS information theory experts.

    Obfuscationists would be more like it. I pointed out to Patrick the incoherence of saying that entropy is both information and missing information. His response:

    There is no “missing” information. Despite what Ben-Naim is proposing, entropy and information are defined by Shannon and are related to Boltzman’s entropy and thermodynamic entropy as described in the above paper. You are trying to dislodge 70 years of information theory and 150 years of thermodynamics with your nonsense. You are not an expert in this field, not even a novice. Plus you are not interested in learning even the foundations of the field. It is a waste of time discussing Information Theory with you.

    LoL.

    And of course Joshua:

    Thermodynamics helps immensely. It does not confuse the issue. I highly encourage bringing it in. If you can’t understand how information theory is connected to thermodynamic entropy, you do not understand information theory.

  130. 130
    EricMH says:

    @Mung, Patrick and Joshua should take it up with Li and Vitanyi. Apparently, Li and Vitanyi are dislodging 70 years of information theory, too.

    From their book ‘An Introduction to Kolmogorov Complexity and Its Applications’,

    “By choosing a particular message a from S, we remove the entropy from X by the assignment X := a and produce or transmit information I = log d(S) by our selection of a.”

    In other words: information = removal of entropy by assigning a particular outcome.

  131. 131
    gpuccio says:

    EricMH at #125:

    I am not sure I agree with you.

    Let’s tale a computer program which has been compressed as much as possible. In that form, it is not compressible, and yet it retains all its function.

    Moreover, the function of a long and complex protein depends on its specific sequence, and not on its limited compressibility. In many cases we have proteins that have extremely high functional complexity, but rather low compressibility.

    Therefore, function is a completely different concept.

    Order can be due to design, but it can also be due to necessity.

    Complex function, instead, is always a marker of design.

  132. 132
    EricMH says:

    @gpuccio, I think we’re just talking about different sides of the same coin. The elegant program for a compressible bitstring is not compressible, but the bitstring it generates is. DNA is the equivalent of an elegant program, which would make the protein it generates equivalent to the compressible bitstring.

    So then we’d measure order by the compressibility of the protein or all the proteins created by DNA, which is incredibly high, since DNA results in a living organism, and the probability of the living organism being assembled through physical processes independent of the DNA is essentially nil. We can lower bound the self information of this probability with the mass of the organism and upper bound the Kolmogorov complexity of the DNA by the mass of a single DNA strand.

    Plugging this into the CSI formula gives us:

    CSI(organism) > mass of organism – mass of DNA ~ mass of organism

  133. 133
    Nonlin.org says:

    SA @122

    Darwinism and its neo fails all tests:
    Gradualism fails – http://nonlin.org/gradualism/
    Natural selection fails – http://nonlin.org/natural-selection/
    Divergence of character fails – http://nonlin.org/evotest/
    Speciation fails – http://nonlin.org/speciation-problems/
    DNA “essence of life” fails – http://nonlin.org/dna-not-essence-of-life/
    Randomness fails – http://nonlin.org/random-abuse/
    Abiogenesis fails – http://nonlin.org/warmpond/
    Science against Religion fails – http://nonlin.org/philosophy-religion-and-science/
    etc., etc.
    And let’s test it again and make sure it fails again and again: http://nonlin.org/evotest/

  134. 134
    Nonlin.org says:

    EugeneS @124 126

    Because order is fundamentally NOT function.

    This is wrong. Function is order. Yes, order need not be function.

    Agree with your examples. So when you see dunes don’t you NEED to know their origin? Something/Someone caused them. And when you see the same dunes encrusted on a cave wall, are they not designed?

  135. 135
    Nonlin.org says:

    KF @114,

    we properly distinguish order which may have low information content [e.g. asasas . . .] from functionally coherent and complex integrated organisation

    So when you see “asasas . . .”, do you…:
    a) stop and wonder?
    b) don’t pay any attention?

  136. 136
    EricMH says:

    @Nonlin.org, I agree with why you say NS doesn’t exist. Only Lamarckianism exists. Great point. There is no reproducing digital code in nature apart from living organisms, and all living organisms are purposeful. Therefore, only purposeful selection ever takes place. I believe that is a categorical disproof of Darwinian evolution.

    http://nonlin.org/natural-selection/

    Per your general point that all order signifies intelligence, you are correct if you assume a uniform prior, since most bitstrings are incompressible. How do you justify a uniform prior?

    How would you characterize intelligent agency? What distinguishes it from chance and necessity?

  137. 137
    Silver Asiatic says:

    Nonlin @133

    I only read your NS analysis and it does expose many of the problems.

    The concept was meant to be a parallel to artificial selection with “nature” doing the selecting instead of a breeder.

    But as explained, nature does not select features and every population will have a mixture of more or less fit. The exact, unchanged feature in an organism can be better or worse adapted to changing environmental conditions over a lifetime (or generations).

    If environmental changes are cyclical, then adaptations to the environment will end in stasis.

    Competition for resources is not a zero sum game with winners getting everything and losers going extinct.

  138. 138
    EricMH says:

    @Nonlin.org, while I agree with a lot of your conclusions, the purposes of ID are a bit different. The goal is to make these sorts of arguments quantitative and empirical, i.e. move the arguments out of the realm of philosophy and get scientific results from them. Sort of like Newton discovered the laws of physics based on the philosophical premise that God ruled the physical world in a lawful manner, a Catholic priest invented the idea of the big bang, another Christian invented wave particle duality to explain the dual nature of Christ, etc.

    I would like to take ID even further and reduce it not only to science, but also to technology. This should be doable in numerous areas, especially my own field of computer science, and is already being done such as in the area of human computation.

    So, the overall goal of ID is not just to make arguments, but to reduce theory to practice.

    I’d be interested in what ways your theories could be reduced to practice.

  139. 139
    gpuccio says:

    EricMH:

    I think, instead, that there is a big difference between your point and my point.

    If the AAs in a protein are arranged to perform a function, that is the source of specification. Design has the purpose of attaining the function, not the purpose of generating compressible order. Therefore, function and not order is the marker of design.

    If the purpose of design is to generate order, then you are right. For example, a designer can simply order a deck of cards. In that case order, if it cannot be explained by simple necessity laws in the system, is a good marker of design.

    But when function is the purpose, order is not important. A watch is a watch because it is assembled to measure time, not because it is an ordered object. There could be thousands of similar ordered objects that could not in any way measure time, and probably implement no other complex function.

    Focusing on order in biological objects is a big error of perspective.

  140. 140
    gpuccio says:

    EricMH at # 136:

    “How would you characterize intelligent agency? What distinguishes it from chance and necessity?”

    Well, you did not ask that to me, but I would like to give a simple answer just the same.

    Intelligent agency is conscious. It acts by conscious representations. Its interventions on matter are preceded by conscious representations, are guided by the conscious experience of understanding meaning and by the feeling experience of having purposes.

    The problem is not to define chance, necessity and design as logical alternatives. The problem is to analyze empirically what a non conscious system can do and what a conscious system can do. Chance and necessity are always present, both in non conscious systems and in conscious systems. But the intervention of intelligent and purposeful consciousness, which does not obey the mere laws of chance and necessity, makes all the difference.

    Bt the way, believe me, NS does exist. It is a process that can be well observed. For example in antibiotic resistance.

    To say differently is to ignore the basics of science.

    What NS can or cannot do, of course, is all another matter.

  141. 141
    gpuccio says:

    Nonlin.org:

    “This is wrong. Function is order. ”

    Nonsense.

    Function is much more than order, even if it usually requires some order.

    Remember that the only way to define order is through compressibility.

    Your “clear definition” of order at #103:

    “the arrangement or disposition of people or things in relation to each other according to a particular sequence, pattern, or method”

    is absolutely vague and useless.

    Take a Shakespeare sonnet, and compare it to a piece of English text of similar length, generated by a random selection of English words and punctuation.

    Both are in some way ordered (they are both made of correct English words, but the sonnet expresses deep meanings, while the random text expresses practically nothing. The difference is in the meaning, not on the order.

    Even is you build a piece of text that obeys the rules of grammar and syntax, it could still have no meaning.

    “The river is eating while eight stones are dying”

    is a perfectly ordered sequence, but still it means very little.

    “The ratio of the circumference to its diameter is a transcendental number called pi”

    is a similarly ordered sequence, but its meaning is extremely more specific and “functional”.

    Order is of little importance here. Meaning and function (respectively the property of descriptive information and prescriptive information) are the real thing.

  142. 142
    EricMH says:

    @gpuccio, not really clear what you disagree with. I do agree that the purpose of DNA is the function, not the order. But that does not negate the fact there is a whole lot of compressible order in an organism. Maybe the problem is because we associate the word ‘order’ with straight lines and geometric shapes, whereas the organic world is anything but. Another word like ‘fecund’ or ‘generative’ is probably better. At any rate, the CSI analysis still works in the case of biological organisms.

    Regarding NS, you maybe should read Nonlin’s argument. I think it makes sense. Even in the case of antibiotic resistance the bacteria are purposeful in their actions, so teleology is influencing the selection.

    Finally, if you think that intelligent agency can be reduced to chance and necessity, then we are not really proposing anything different than materialists. We are just saying there aren’t enough probabilistic resources, and then we fill the gap with ‘god’, which would justly be characterized as god-of-the-gaps. On the other hand, if intelligence cannot be reduced to chance and necessity, then it is indeed a logical alternative to the two, and has different and detectable physical characteristics.

  143. 143
    Nonlin.org says:

    ErichMH @136 @138

    If you refer to epigenetics as Lamarckianism, let’s not forget those effects only last a few generations.

    I am not sure what you mean by “uniform prior”. Randomness? If so, design doesn’t need an “uniform prior”. For instance, we metabolize a variety of raw materials.

    I would add “chance” and “necessity” to the list of amat made-up concepts. There is no perfect randomness out there (for instance 6-face die is random within designed limits) and “necessity” means what? Who declares something a “necessity” or not? Maybe math and logic qualify as necessity to us mortals, but to God? How about gravity and sexual reproduction? Are those “necessity”? To me, those are just rules of the kind intelligent agents make.

    I agree with you on going beyond philosophy and into quantifiable proofs. First decision block in my design detection diagram is as quantifiable and scientific as it gets. I am still thinking about improving the rest…

    One thing is for sure, every time the Darwinists write a piece of software that supposedly “evolves”, they sneak in the designer and claim none was involved. The other thing is that everyone equates ‘data’ with ‘information’ when in fact data need not carry information. This helps them spread confusion. And spreading confusion is what Darwinism is all about.

  144. 144
    Nonlin.org says:

    gpuccio @141

    You didn’t read all:
    “function is order. Yes, order need not be function.”

    Not my definition. It may not be perfect, but where’s a better one?

    Re: “Shakespeare sonnet vs random selection” (debatable if a good example), fits very well with my: “function is order, but order is not necessarily function”.

    Meaning is user dependent (there is no universal “meaning”). Shakespeare (in English) means nothing to a cat or to non-English speaking Chinese.

    If “you build a piece of text that obeys the rules of grammar and syntax”, then you are The Designer, even if it has no meaning to anyone. Let’s call it ‘poetry’. Even if you build an AI system that does the same, the creator is still YOU, not the machine. AI is just a tool like a pencil or typewriter.

    “Descriptive/prescriptive information” is still unconvincing. And again, data is not information.

  145. 145
    jawa says:

    Off topic:

    Apparently this OP has been closed for comments. Is that right?

    JVL had posted continuously between October 6 and 15, promising to come back to comment on gpuccio’s explanations, but we have been left waiting for the continuation of that debate.

    The last post by gpuccio in that thread was dated October 24. No more posts appeared after that date.

  146. 146
    PaoloV says:

    After reading gpuccio @141, I had this question:

    Can a function exist as a purpose (intention) before being associated with any physical object or system?

    Let’s say for example:

    1. we want to make this place pleasant to the people who visit it.
    2. we want to move people from one place to another
    3. we need to move cargo from one location to various distant places
    4. we want to keep babies from reaching certain places in the house
    5. we want to educate children
    6. we want to protect people from stormy weather
    7. we want to improve our hearing and vision

    We could be more specific in some cases.

    Based on those general functional purposes, we could design, develop, test, implement thing and systems, in order to meet those goals.

    The designed systems could include components that have more specific functions.

    Just thinking out loud. Well, not so loud really, because my keyboard is quiet. 🙂

  147. 147
    gpuccio says:

    Nonlin.org:

    I did read it all. I did not quote:

    “Yes, order need not be function.”

    because that’s the part I agree with.

    The part I don’t agree with is:

    “function is order.”

    So, that’s the part I commented on.

    Because that’s the part that is wrong.

    Because, in most cases, function has nothing to do with order. It has to do with the thing to be accomplished.

    The better definition for order is compressibility. That’s something that can be used and measured in science.

    In my example of Shakespeare’s sonnet, the random text and the sonnet share the same type of order. So, why is the sonnet so meaningful? Its added meaning does not depend on any type of ordered compressibility.

    The same is true for a highly compressed program. It is not compressible, it is not ordered in any particular way, but it retains its full function.

    The same is true for a protein. The sequence of AAs is usually scarcely compressible. Take for example an intrinsically disordered proteins, which has not even the scarce regularities that are usually associated to some forms of folding. And yet it can be extremely functional.

    Function does not depend on order, but on the intentional association of the sequence to some task to be achieved.

    It is not true that meaning is user dependent. A Shakespeare sonnet is not user dependent. It has its meaning in all cases. Of course, you have to be aware of some keys to understand it, for example English language.

    But it is completely wrong to say that its meaning is user dependent. It’s a gross philosophical error. It’s like saying that the function of a motor car is user dependent only because a cat cannot drive.

    You do bad philosophy, and nothing else.

    OK, to put an end to this waste of time, I will just adopt your type of arguments:

    What you say is unconvincing. Period.

  148. 148
    gpuccio says:

    EricMH at #142:

    It may not be clear to you, but I believe that we do disagree on some important things. Nothing bad in that, but it is always better to be aware of the differences rather than to ignore them.

    You seem to believe that CSI and functional information are different things.

    That’s not true. FI is a subset of CSI.

    I see things this way.

    CSI is any type of information for which you can give some type of specification.

    A specification is any rule that generates a binary partition in the search space in some well defined system.

    Any specification can be used to infer design, if we observe an object which exhibits CSI beyond some appropriate threshold, usually 500 bits, computed as -log2 of the ratio between target space and search space for that specification. Whatever the type of specification used.

    But, as Dembski makes clear in his filter, we must also reasonably exclude necessity as an explanation for our specification of the target space.

    CSI has different flavours, according to the type of specification we use.

    One possible subset of specification is based on order (compressibility). This is only a subset of CSI. It has a serious limit, because it can detect design efficiently only if order itself was the purpose of the designer. For example, it can well detect design in an ordered deck of cards. Or in a mathematical progression. Another limit is that we must seriously exclude necessity here, because necessity can generate order. So, while it is rather unlikely that some necessity law can explain an ordered deck of cards, mathematical progressions could originate by necessity, in some contexts.

    Functional information is another important subset of CSI. We could divide it into meaningful information and functional information proper, according to the purpose of the specified information (meaning for descriptive information, function for prescriptive information).

    In functional information, the purpose of the designer is to achieve a function, not to generate order. Maybe some order is necessary to implement the function, maybe not. In all cases, here it is function, and only function, that correlates with the designer’s intentions. Therefore, it’s function, and only function, that we must use as specification.

    That’s the case for all machines, for all computer programs, and of course for biological objects.

    I hope that’s clear.

    As you say that your purpose is to “move the arguments out of the realm of philosophy and get scientific results from them”, and to reduce theories to practice, here is a very practical example.

    I have computed CSI as functional information for many proteins. Let’s take a classical example. The alpha and beta chains of ATP synthase.

    Using an indirect method based on conservation of the sequence from bacteria to humans, I have computed CSI as functional information for those two proteins as follows:

    alpha chain = at least 561 bits

    beta chain = at least 663 bits

    total = at least 1224 bits

    Therefore, I infer design for both of them, and even more strongly for the irreducibly complex machine generated by both.

    Could you please explain how you would compute CSI for those two proteins, using a specification based on order and compressibility?

    Thank you.

    Finally, I have never said that “intelligence cannot be reduced to chance and necessity”. Not at all.

    What I said is:

    “The problem is not to define chance, necessity and design as logical alternatives. The problem is to analyze empirically what a non conscious system can do and what a conscious system can do. Chance and necessity are always present, both in non conscious systems and in conscious systems. But the intervention of intelligent and purposeful consciousness, which does not obey the mere laws of chance and necessity, makes all the difference.

    Emphasis added.

    My point is that design is not a “logical alternative”. It is an empirical alternative, whose powers can and must be assessed by empirical observations. It is an observed process that can generate things (like functional information) that other observed processes (non conscious systems) can never generate.

    These are, IMO, the difference.

    About antibiotic resistance, if you really think that choloroquine resistance, as discussed in detail by Behe in “The edge of evolution” and also by me here:

    What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/

    is not an example of NS, I will not waste any more time about that. You are entitled to your opinion, and can go on believing, as Nonlin.org, that NS does not exist.

  149. 149
    Bob O'H says:

    EricMH @ 100 –
    (sorry for the gap in replying)

    @Bob O’H, CSI hasn’t changed dramatically, I just added another term for the specification. The rest is the same. The dependency issue is taken care of by establishing a penalty for dependency, which is the size of the specification.

    OK, so we’re back to the log N you introduced at 92. But you haven’t responded to my comments at 93: this CSI is subjective, and applies to all CSIs looked at (so there is no penalisation, only a constant shift). I can’t see how the (constant) penalty takes care of the dependency: you still end up with the same specification, just with a value of CSI that is shifted by log N.

    I had to add the dependency penalty because currently there is no well established approach to quantifying how independent a specification is. In the objective case we have to consider all possible specifications, because they are no longer limited by what humans can dream up.

    What? At 47 you wrote “The key to avoid the dilemma you present is the specification must be independent of the event. If we just enumerate all possible specifications, and pick the one that matches the event, then the specification is no longer independent from the event. As such, the set of valid specifications has to be a subset of the possible specifications. ”

    So, we have to look all specifications, and also have to only look at a subset.

    In the subjective case, independence was a heuristic. We just assumed descriptive language of some unrelated phenomena, such as human designed artifacts, were independent of biological phenomena that we’d never discovered before. Seems reasonable enough. But it isn’t a quantitative heuristic. I just made specification dependence quantitative so we can talk about the objective CSI that is independent of observers.

    OK, fair enough. But it would be good to account for dependence in a way that makes some sense.

    Addressing the math. Since we’re minimizing over all S, we can remove the S from oCSI, giving just oCSI(X,P).

    Minimising or maximising? (this is only a sign shift anyway!)

    What we want is to guarantee E[oCSI(X,P)] <= 0, so that give enough measurements we can definitively eliminate P as a valid source of X, and that criterion is met by oCSI.

    What is P? And why is 0 such an important value?

  150. 150
    gpuccio says:

    EricMH and Nonlin.org:

    Just a simple example from mathemathics to clarify better one of the aspects:

    1) A Fibonacci sequence (30 numbers):

    0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377, 610, 987, 1597, 2584, 4181, 6765, 10946, 17711, 28657, 46368, 75025, 121393, 196418, 317811, 514229

    2) The first 30 decimal figures of pi:

    3.14159265358979323846264338327

    1) is ordered and compressible. 2) is neither.

    And yet, 2) conveys a very important mathematical information. Its functional information is easily computed as about 100 bits.

    How could you specify the functional information in 2) using order and compressibility?

  151. 151
    kairosfocus says:

    EMH, distinct identity is tied to quantity and to structure [general sense, e.g. the Von Neumann construction from {} –> 0, {0} –> 1, {0,1} –> 2 etc gives a set theory based structure for natural counting numbers which can be extended to the surreals]. Thus, it is framework to both mathematics and reasoning in general. Indeed, Law of Identity, non-contradiction and excluded middle (boundary) are mutually instantly present as facets of distinct identity. My point is, such are framework to any distinct world existing and are cases of necessary entities, necessary being. We need to have a frame of thought in which necessary being is acknowledged as a legitimate facet of the logic of being, in order to begin to understand many things that otherwise will seem strange or dubious. Some of that cropped up above. KF

  152. 152
    kairosfocus says:

    NL (et al),

    order implies a rational principle; it points to the principle of sufficient reason in at least a weak sense on which we do not presume that we know or readily discern order. That is a key start-point.

    “AS, repeat” is a string example of a unit cell structure familiar from crystals. It is of low information content, write AS repeat in a suitable language with associated mechanisms or machines and you get the pattern.

    A random string essentially is replicated by quoting it. It is resistant to compression and in that sense has high information content. However, it does not have an interior explanatory principle that can lead us to replicate save by quoting.

    Functionally specific, coherent organisation of some complexity is distinct and was identified as such by Orgel and Wicken in the 70’s. Here, it is not simple repetitive unit cells, we have structures arranged to attain a particular outcome dependent on configuration. Thus, sentences such as the last. There are organising principles, there is a result from the config acting in a context [intelligible communication, protein construction and function, a working ABU 6500 C3 fishing reel etc], and the function can be separately and “simply” described, leading to target zones in large config spaces of possible lumped or scattered combinations of string elements.

    Strings, of course, are WLOG as the old animal, veg or mineral party-game illustrates. That is, a suitable description language and chain of Y/N q’s will allow specification, description and structuring. AutoCAD etc do this all the time. Where, the reasonable string length is an index of complexity. It also indicates difficulty of finding successful configs in the space of possibilities on gamut of sol system or observed cosmos. Thus, 10^17 s, 10^12 – 15 tries per s for atomic-molecular scale interactions, 10^57 to 10^80 atoms to play with. Thence, a threshold where if a functionally specific complex entity has 500 – 1,000 bits of complexity [not all cases can be readily calculated even as full solutions in q-mech can be hard to come by] it is maximally implausible that such FSCO/I came about by blind chance and or mechanical necessity. Blind needle in haystack search has its limitations.

    However, intelligently directed configuration — design — routinely produces such. As your comments in thread exemplify.

    So, function based on particular arrangement from a large field of possibilities is a key and reasonable concept.

    KF

  153. 153
    Bob O'H says:

    gpuccio @ 150 – you could express pi as an algorithm to calculate it (same for Fibonacci numbers, of course).

  154. 154
    daveS says:

    Bob O’H,

    you could express pi as an algorithm to calculate it (same for Fibonacci numbers, of course).

    This suggests to me a broader question: Do we know of any specific incompressible strings with length comparable to gpuccio’s examples? Incompressibility is undecidable, but I don’t know whether you can actually write down particular instances of incompressible strings. 10 minutes of furious googling has not helped. 🙂

  155. 155
    gpuccio says:

    Bob O’H:

    Of course, but I think that it would be longer than 100 bits, even if I am not an expert. So, the Kolmogorov complexity of that string remains the complexity of the string itself. That is probably not true for the Fibonacci series, which can be easily computed.

    Of course, if we increase the number of the digits of pi in the string, there will be a point where the string is more complex than the algorithm to generate it. Then, and only then, the Kolmogorov complexity of the string becomes the complexity of the generating algorithm.

    I have often used that example to show that algorithms cannot really generate new functional complexity, because the Kolmogorov complexity of what they generate is, at most, the complexity of the algorithm itself.

  156. 156
    gpuccio says:

    daveS:

    I am not a mathematician, but I think that absolute incompressibility cannot really be proven.

    However, as we are interested in empirical science here, it’s more than enough to consider the most compressed string that is available. That will do for our purposes.

  157. 157
    ET says:

    Bob O’H:

    you could express pi as an algorithm to calculate it

    Let’s see it to see if you really have something there.

  158. 158
    gpuccio says:

    Bob O’H:

    Here is a simple program to generate Fibonacci series:

    //Fibonacci Series using Recursion
    #include
    int fib(int n)
    {
    if (n <= 1)
    return n;
    return fib(n-1) + fib(n-2);
    }

    int main ()
    {
    int n = 9;
    printf("%d", fib(n));
    getchar();
    return 0;
    }

    I am not sure how many bits that would be, once compiled. But probably less than 100 bits.

    And however, the series of 30 Fibonacci numbers is more complex than 100 bits.

  159. 159
    gpuccio says:

    Bob O’H:

    It seems that computing the first 800 digits of pi can be done with 160 bytes.

    https://crypto.stanford.edu/pbc/notes/pi/code.html

    In that case, the complexity of the output would be 2657.5 bits, while the Kolmogorov complexity of the same string would be only 1280 bits.

  160. 160
    daveS says:

    gpuccio,

    I am not a mathematician, but I think that absolute incompressibility cannot really be proven.

    That’s more or less what I recall as well, although I don’t know details. I think EricMH has gone over this in a previous discussion.

    Going back to your example, there is an “obvious” and simple way to describe the first several terms of the Fibonacci sequence. I believe there exist as well such algorithms/formulas for the digits of pi, so that given the first n digits, you can find the n + 1st, but they are complicated. So I understand your point.

    On the other hand, it’s not clear to me that we know there is a sharp distinction between the two sequences.

  161. 161
    gpuccio says:

    ET:

    I think my #159 answers your question.

  162. 162
    gpuccio says:

    daveS:

    My point is that the Fibonacci series is strongly compressible. I don’t know exactly how many bits the program I quoted would be when compiled, but it does not seem very complex. So, any Fibonacci series can be generated by that number n of bits.

    The series of pi digits that I have shown, instead, is not compressible. It has no intrinsic order. OK, it is only 100 bits. But if, as I have shown, a simple program to generate the digits of pi is about 1280 bits (maybe there are simpler ones, maybe not, again I am not an expert), then any sequence of pi digits above 500 bits will allow a design inference, even if not compressible. And if it is compressible, it will allow a design inference not because it is compressible, but for the opposite reason: because the simplest known algorithm that can generate it is, however, longer than 500 bits and is not compressible (at least empirically).

    That should clarify even further that function has really little to do with order and compressibility.

  163. 163
    daveS says:

    gpuccio,

    First, I do find what you are saying to be plausible, and I don’t have enough knowledge to dispute any of it.

    We know:

    1) There are algorithms which generate the Fibonacci numbers

    2) There are algorithms which generate the decimal digits of pi in order

    As you point out, the Fibonacci algorithm is very short and simple. The known algorithms to generate digits of pi in order are, as far as I know, much more complicated (and lengthy) and would be of no use in attempting to compress the first 30 digits of pi.

    That’s all consistent with what you say.

    The only question I have is whether we can actually verify that those 30 digits of pi form an incompressible string. That requires a mathematical proof of some sort. Until that has occurred, I’m not comfortable agreeing that it is in fact “incompressible”.

  164. 164
    lantog says:

    Hi Everyone

    Off topic but something I think will be of interest to everyone. Stephen Meyer has a new talk posted. Search youtube for “Intelligent Design 3.0” and “Meyer”. Axe also speaks for a bit.
    This is the best single presentation of ID I’ve ever seen (and I’ve seen most of them) and its current ( 4 mo old) and he discusses some of his current research projects.
    I can’t imagine how all you regulars missed this..anyway, trust me, you’ll love it… and I’m not an ID supporter!

  165. 165
  166. 166
    ET says:

    gpuccio- There are more than 800 digits in pi

  167. 167
    lantog says:

    Isn’t pi compressible for the same reason the Fibonacci series is: its expressible as 22/7 ?

  168. 168
    daveS says:

    22/7 does agree with the first three (decimal) digits of pi, and the first four characters if you include the decimal point. After that position, pi and 22/7 usually disagree however.

  169. 169
    gpuccio says:

    daveS:

    “Pi has been calculated to over one trillion digits beyond its decimal point. As an irrational and transcendental number, it will continue infinitely without repetition or pattern.”

    https://www.piday.org/

    “Being an irrational number, ? cannot be expressed as a common fraction (equivalently, its decimal representation never ends and never settles into a permanently repeating pattern). Still, fractions such as 22/7 and other rational numbers are commonly used to approximate ?. The digits appear to be randomly distributed. In particular, the digit sequence of ? is conjectured to satisfy a specific kind of statistical randomness, but to date, no proof of this has been discovered. Also, ? is a transcendental number; that is, it is not the root of any polynomial having rational coefficients. This transcendence of ? implies that it is impossible to solve the ancient challenge of squaring the circle with a compass and straightedge.”

    https://en.wikipedia.org/wiki/Pi

    pi is probably one of the most incompressible numeric sequences you can find.

    For all practical purposes, we don’t need a mathematical proof that it is absolutely incompressible. For all practical purposes, no significant compression is known or available. That’s enough.

  170. 170
    gpuccio says:

    lantog:

    see my previous comment.

  171. 171
    gpuccio says:

    ET:

    There are infinite digits in pi.

    However, each sequence of n digits is an approximation, and it has a definite complexity. All out reasonings here are about finite strings of numbers, and their complexity.

  172. 172
    gpuccio says:

    To all:

    All the things we have said are simply proof of my point:

    Sequences that are practically incompressible can have high function, therefore high functional information, therefore high CSI, and allow an easy design inference.

    Functional specification is not related to order or compressibility.

  173. 173
    daveS says:

    gpuccio,

    Certainly the two paragraphs you have quoted are accurate. The part about “no pattern” might be arguable, but that’s beside the point here.

    pi is probably one of the most incompressible numeric sequences you can find.

    For all practical purposes, we don’t need a mathematical proof that it is absolutely incompressible. For all practical purposes, no significant compression is known or available. That’s enough.

    Can you sidestep this issue simply by saying that the string consisting of the first 30 digits of pi is not known to be compressible? If that suffices, can we just go with that?

    The way you are currently using the terms, I’m afraid that actual mathematicians (as opposed to myself) are going to pounce on this. Unless there actually is a proof that it’s incompressible, of course!

    PS: A correction to my post #160, about certain algorithms for generating the digits of pi. Here is a more accurate description:

    The spigot algorithm for calculating the digits of π and other numbers have been invented by S. Rabinovitz in 1991 and investigate[d] by Rabinovitz and Wagon in 1995. The algorithm generates the digits sequentially, one at a time, and does not use the digits after they are computed.

  174. 174
    gpuccio says:

    daveS:

    “Can you sidestep this issue simply by saying that the string consisting of the first 30 digits of pi is not known to be compressible? If that suffices, can we just go with that?”

    Sure. That’s what I mean.

    I just say that it is empirically non compressible. Where “empirically” just means “as far as we can judge from known facts”.

    There is a big difference between a mathematical proof and an empirical inference. Empirical inferences must be based on what we know. It’s one of the tricks of neo-darwinists to ask, when really cornered, that ID should prove something beyond any possible doubt. For example, that neo-darwinian pathways to complex function don’t exist.

    But that’s not how empirical science works. For empirical science, the simple fact that those pathways have never been observed, or even simply reasonably traced, is more than enough to make them an explanation usupported by known facts.

  175. 175
    gpuccio says:

    To all:

    This program is very good and very fast.

    http://numbers.computation.fre.....ifast.html

    It can compute a large number of pi digits very quickly, and with different algorithms.

    The uncompressed program is 328 KB long.

    The compressed (zipped) version is 153 KB long.

    Certainly not the simplest solution, but a very good one.

  176. 176
    EricMH says:

    @gpuccio, I agree you can have FI without compressibility, and it is a subset of CSI. The function is just another specification, as you say. But, order can also be indicative of intelligent design in the right scenario (i.e. the chance hypothesis is a uniform distribution over 1000 coin flips, but we get all heads), though perhaps this is not relevant for biology. I don’t know much about the biological details, so cannot comment there. My point is that Nonlin is correct in saying that order can be indicative of intelligent design. Incidentally, disorder can also be indicative of intelligent design. At any rate, I don’t believe there is a true disagreement between us, or even with Nonlin, although I guess we can disagree on whether we truly disagree 😀

  177. 177
    EricMH says:

    @Bob O’H, my apologies for the confusion I’ve introduced. I hadn’t considered a completely objective CSI measure before, so have been developing the idea as I go.

    The difference between my seemingly contradictory statements about enumerating all possible specifications is in the most recent case I’ve introduced the penalty term, which solves the dependency problem.

    The importance of the E[oCSI] formula is that CSI is supposed to guarantee (at least probabilistically) that if CSI > 1 then intelligent agency is the best explanation for the event, based on the idea that 2^-CSI is an upper bound on the probability of observing an event with that amount of CSI given the chance hypothesis. So, CSI > 1 means the probability 1 does not imply intelligent agency is the more likely explanation. This is, in fact, a problem with Dembski’s original version of CSI, because we can construct scenarios where the expected CSI is infinite. Ewert’s ASC variant of CSI corrects this problem and guarantees the expectation is non positive, since his use of prefix free Kolmogorov complexity satisfies the Kraft inequality.

    The oCSI I propose is a further elaboration on Ewert’s ASC concept, where the size of the specification is also included in the calculation, since Ewert does not quantify independence in his work. Including the specification as K(X,S) maintains ASC’s original guarantee of non positive expectation since K(X,S) >= K(X), and K(X) follows the Kraft inequality.

    Regarding minimization, I mean finding the S such that K(S) is minimal. This is the same as maximizing oCSI over all possible S.

    P is the chance hypothesis.

  178. 178
    EricMH says:

    Error in my last comment:

    > So, CSI > 1 means the probability 1 does not imply intelligent agency is the more likely explanation.

    Should be:

    So, E[CSI] > 0 means CSI > 1 does not imply intelligent agency is the more likely explanation.

  179. 179
    EricMH says:

    @Mung, here’s a quote from Papoulis, who wrote the book on random processes and variables. He says “uncertainty equals information”, but what he means is the quantities are the same, not that the concepts are the same. Papoulis is actually saying what you are saying, that “entropy is the lack of information,” since we only get information once the experiment is performed.

    “In the heuristic interpretation of entropy, the number H(A) is a measure of our uncertainty about the event A1 of the partition A prior to the performance of the underlying experiment. If the experiment is performed and the results concerning A1 become known, the uncertainty is removed. We can thus say that the experiment provides information about the events A1 equal to the entropy of their partitions. Thus uncertainty equals information and both are measured by the sum in (15-1).”

  180. 180
    gpuccio says:

    EricMH:

    I agree with your #176 (except about Nonlin! 🙂 )

    I have never denied that that can be indicative of intelligent design. See, for example, my #148:

    “One possible subset of specification is based on order (compressibility). This is only a subset of CSI. It has a serious limit, because it can detect design efficiently only if order itself was the purpose of the designer. For example, it can well detect design in an ordered deck of cards. Or in a mathematical progression. Another limit is that we must seriously exclude necessity here, because necessity can generate order. So, while it is rather unlikely that some necessity law can explain an ordered deck of cards, mathematical progressions could originate by necessity, in some contexts.”

    So, we agree on that too.

    For biology, I believe that function is the real thing.

  181. 181
    gpuccio says:

    Ehm, at #180 it should be:

    I have never denied that order can be indicative of intelligent design.

  182. 182
    EricMH says:

    @gpuccio, great! All Nonlin is doing is restricting the range of specification to Kolmogorov complexity, and assuming something like a uniform prior. Which is a valid CSI metric, if he can justify the uniform prior, which seems pretty plausible with the maximum entropy principle. It’s what most CSI writers do, anyways.

  183. 183
    gpuccio says:

    EricMH:

    He is doing many other things, IMO. None of which I like.

    But OK, let’s leave it to that. 🙂

  184. 184
    EricMH says:

    @gpuccio, agreed. I’m curious to learn more about functional information, in particular how the probability and specification are calculated. Do you recommend any resources?

  185. 185
    gpuccio says:

    EricMH:

    At the cost of being accused of shameless self-promotion, I can recommend my OPs here.

    Here are the main ones, in some order:

    Defining Design

    https://uncommondescent.com/intelligent-design/defining-design/

    Functional information defined

    https://uncommondescent.com/intelligent-design/functional-information-defined/

    An attempt at computing dFSCI for English language

    https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/

    Natural Selection vs Artificial Selection

    https://uncommondescent.com/intelligent-design/natural-selection-vs-artificial-selection/

    Homologies, differences and information jumps

    https://uncommondescent.com/intelligent-design/homologies-differences-and-information-jumps/

    The highly engineered transition to vertebrates: an example of functional information analysis

    https://uncommondescent.com/intelligent-design/the-highly-engineered-transition-to-vertebrates-an-example-of-functional-information-analysis/

    The amazing level of engineering in the transition to the vertebrate proteome: a global analysis

    https://uncommondescent.com/intelligent-design/the-amazing-level-of-engineering-in-the-transition-to-the-vertebrate-proteome-a-global-analysis/

    What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/

    What are the limits of Random Variation? A simple evaluation of the probabilistic resources of our biological world

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-random-variation-a-simple-evaluation-of-the-probabilistic-resources-of-our-biological-world/

    Defending Intelligent Design theory: Why targets are real targets, probabilities real probabilities, and the Texas Sharp Shooter fallacy does not apply at all.

    https://uncommondescent.com/intelligent-design/defending-intelligent-design-theory-why-targets-are-real-targets-propabilities-real-probabilities-and-the-texas-sharp-shooter-fallacy-does-not-apply-at-all/

  186. 186
    gpuccio says:

    EricMH:

    I have answered, with a list of some of my OPs here about the argument of functional information and its applications to biology.

    As usual, the comment is awaiting moderation because of the many links. But it will appear, sooner or later. 🙂

    I think that Behe, Meyer, Axe, Abel and Trevors and Durston are very good sources about that topic. You certainly know them. This paper by Durston is specially important, IMO:

    Measuring the functional sequence complexity of proteins

    https://tbiomed.biomedcentral.com/articles/10.1186/1742-4682-4-47

    And this Szostak paper (from the other side!) is very useful too:

    Functional information and the emergence of biocomplexity

    http://www.pnas.org/content/104/suppl_1/8574

  187. 187
    Nonlin.org says:

    gpuccio @147,

    You keep insisting function is not order, but:
    1. Function:”In mathematics, a function is a relation between a set of inputs and a set of permissible outputs with the property that each input is related to exactly one output.”
    2. Order: “the arrangement or disposition of people or things in relation to each other according to a particular sequence, pattern, or method.”

    When you arrange according to a method, you apply a function to create order. Hence, “function is order”.

    What has ‘compressibility’ to do with order and function? You can have a function f(x) = rand() + x …and we only compress data, not information. Try to “compress” a ‘circle’ if you don’t believe me. But this was discussed before many times …with no impact, sadly.

    Of course meaning is user dependent. The meaning of a Shakespeare sonnet changes with the user and changes with the mood of the same user: sad today -> one meaning, happy tomorrow -> another meaning. Everyone knows it but you. It would be a very boring life if meaning didn’t change.

    The function of a motor car IS user dependent. Today shopping tool, tomorrow entertainment tool, next day sports tool… and teaching tool for teenagers, and terrorist weapon too, etc. Are you serious?

    Again, Fibonacci sequence and Pi are NOT information.

    EricMH: @180

    I see no point in this unnecessary complication called “function”. But if you two are happy with “function”, go ahead and work on it. I just don’t think it will get any traction.

    And anyway, what is “necessity” and who has the power to declare it?

  188. 188
    EricMH says:

    @gpuccio, thanks, I have read through Durston’s paper a bit, as well as Abel’s, and I get the information theory part, but will have to study more to get the biology part. I will look into the Szostak paper too. My impression is the idea is pretty similar to compressed computer code. Do you think DNA is essentially a form of compressed computer code? I look forward to all your links!

    @nonlin, I think part of the problem is the ambiguity of language. If we can reduce our arguments to a mathematical form, then it’ll be clearer. For instance, let’s start with the traditional coin flip scenario. How would you apply your filter to the following sequences?

    1. HHHHHHHHHHHHHHHHHHHH
    2. HTHHTTTHHTTTTTHTTTTT
    3. THHTHHHTTHTHHHTHHHHT

  189. 189
    daveS says:

    Nonlin,

    Again, Fibonacci sequence and Pi are NOT information.

    I would agree with this.

    On the other hand, the Fibonacci sequence and the number pi each have properties. And if I describe some of these properties, then I’ve relayed some information. For example, the sentence “The 11th prime Fibonacci number is 2971215073” does contain information. Do you agree?

  190. 190
    Nonlin.org says:

    EricMH,

    Indeed, ambiguity of language plays a big role. BTW, how do you and gpuccio know that you have a ‘function’ if not from ‘order’? “Every time A happens when B, then C,D,E follow”. I call this order.

    Re. the coin flip, we know from start that only intelligent agents flip coins so there’s your answer 🙂

    But seriously, it depends a lot on the context. Same length sequences have the same probability and that’s why the predetermined sequence to be matched is important. This could be the first set sampled, so if we see any of those sequences repeat over and over then one can forecast the next sample and obviously the sequence is unlikely to be random.

    The example that comes to mind is Pulsars which look like HHHTTTTTTTTTHHHTTTTTTTTTHHHTTTTTTTTT… so now you know what follows at any time.

    If we get any one of your sequences once and then nothing more, I think no astronomer would raise an eyebrow and rightfully so.

    Also, you probably know that never changing signals usually indicate a faulty line, hence Return-to-zero and other such schemes in data transmission.

  191. 191
    Nonlin.org says:

    daveS,

    Information is abstract, user dependent, and resolves an uncertainty, so that would be information if you tell it to your friend or to yourself, but not to your cat/dog.

  192. 192
    kairosfocus says:

    EMH, D/RNA looks and works like machine (object) code, here using prong height as the info bearing element. Interestingly, in 1948, von Neumann envisioned a kinematic self-replicator using a prong-height code. Yale locks use a prong height mechanism, too. KF

  193. 193
    gpuccio says:

    EricMH:

    As my list still does not appear, I will try to send it again, dividing it into three comments. I hope that eludes the need for moderation. Let’s see.

  194. 194
    gpuccio says:

    EricMH:

    (Part 1)

    At the cost of being accused of shameless self-promotion, I can recommend my OPs here.

    Here are the main ones, in some order:

    Defining Design

    https://uncommondescent.com/intelligent-design/defining-design/

    Functional information defined

    https://uncommondescent.com/intelligent-design/functional-information-defined/

    An attempt at computing dFSCI for English language

    https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/

    Natural Selection vs Artificial Selection

    https://uncommondescent.com/intelligent-design/natural-selection-vs-artificial-selection/

  195. 195
    gpuccio says:

    ErciMH:

    (Part 2)

    Homologies, differences and information jumps

    https://uncommondescent.com/intelligent-design/homologies-differences-and-information-jumps/

    The highly engineered transition to vertebrates: an example of functional information analysis

    https://uncommondescent.com/intelligent-design/the-highly-engineered-transition-to-vertebrates-an-example-of-functional-information-analysis/

    The amazing level of engineering in the transition to the vertebrate proteome: a global analysis

    https://uncommondescent.com/intelligent-design/the-amazing-level-of-engineering-in-the-transition-to-the-vertebrate-proteome-a-global-analysis/

  196. 196
    gpuccio says:

    EricMH:

    (Part 3)

    What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/

    What are the limits of Random Variation? A simple evaluation of the probabilistic resources of our biological world

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-random-variation-a-simple-evaluation-of-the-probabilistic-resources-of-our-biological-world/

    Defending Intelligent Design theory: Why targets are real targets, probabilities real probabilities, and the Texas Sharp Shooter fallacy does not apply at all.

    https://uncommondescent.com/intelligent-design/defending-intelligent-design-theory-why-targets-are-real-targets-propabilities-real-probabilities-and-the-texas-sharp-shooter-fallacy-does-not-apply-at-all/

  197. 197
    gpuccio says:

    EricMH:

    OK, it worked! 🙂

    Now, while I leave to you the discussion with Nonlin, I will answer your comment #187. In a moment.

  198. 198
    gpuccio says:

    daveS at #188:

    “I would agree with this.”

    Well, as usual with Nonlin’s statements, I don’t agree at all!

    Both the Fibonacci series and the pi sequence that I have given at #150 are very good examples of meaningful and functional information.

    They are both meaningful because they both convey a specific mathematical meaning. They are, in that sense, universal mathematical objects. Therefore, they are descriptive information, exactly like a Shakespeare’s sonnet.

    But they are also, both of them, functional information (prescriptive information), because they can be used (both of them) in some empirical system to implement specific functions.

    The Fibonacci series that I have presented, for example, (30 numbers), can be used in practical contexts to implement many specific tasks, like the tiling of a surface or the drawing of a spiral. See here:

    https://en.wikipedia.org/wiki/Fibonacci_number

    Of course, the specific object that I have given can be used up to 30 numbers, IOWs has a specific functional information content.

    The sequence of pi digits, of course, can be used to solve a huge number of practical computations: pi is a precious constant in a lot of practical problems that can be solved mathematically. Again, the object I have given can implement that function up to a precision of 30 digits (29 decimals).

    These two objects are good examples of the amazing truth, highlighted here by KF, that mathematical objects, while being in essence abstract, are the foundation for our understanding (and modification) of empirical reality.

  199. 199
    gpuccio says:

    EricMH: at #187:

    I have read through Durston’s paper a bit, as well as Abel’s, and I get the information theory part, but will have to study more to get the biology part. I will look into the Szostak paper too. My impression is the idea is pretty similar to compressed computer code. Do you think DNA is essentially a form of compressed computer code?

    No, again compression has nothing to do with that.

    DNA is, at least for its protein coding part, a redundant code, not a compressed code.

    Let’s take for example a protein coding gene.

    If it codes for a protein that is 100 AAs long, its length will be 300 nucleotides (I am not considering the stop codon here).

    So, we have a potential information content:

    a) In the coding gene: a sequence of 300 in base 4, that is:

    4^300 = 600 bits

    b) In the protein: a sequence of 100 in base 20, that is:

    20^100 = 432 bits

    That’s because the code is redundant. No compression here.

    IOWs, even if a protein sequence could in principle be slightly compressible (but certainly not much, in the general case), that information is certainly not compressed at the DNA level. Indeed, it is not compressed anywhere in biological systems, in general.

    Even proteins that are potentially compressible, like those that have many rather repetitive sub-sequences, are usually translated from genes that have those repetitions too.

  200. 200
    gpuccio says:

    EricMH:

    You can find my explicit definition of functional information, and the general procedure to compute it, in the second OP in my list:

    Functional information defined

    https://uncommondescent.com/intelligent-design/functional-information-defined/

    For your convenience, I will paste here the essential definitions from that OP:

    c) Specification. Given a well defined set of objects (the search space), we call “specification”, in relation to that set, any explicit objective rule that can divide the set in two non overlapping subsets: the “specified” subset (target space) and the “non specified” subset. IOWs, a specification is any well defined rule which generates a binary partition in a well defined set of objects.

    d) Functional Specification. It is a special form of specification (in the sense defined above), where the rule that specifies is of the following type: “The specified subset in this well defined set of objects includes all the objects in the set which can implement the following, well defined function…” . IOWs, a functional specification is any well defined rule which generates a binary partition in a well defined set of objects using a function defined as in a) and verifying if the functionality, defined as in b), is present in each object of the set.

    It should be clear that functional specification is a definite subset of specification. Other properties, different from function, can in principle be used to specify. But for our purposes we will stick to functional specification, as defined here.

    e) The ratio Target space/Search space expresses the probability of getting an object from the search space by one random search attempt, in a system where each object has the same probability of being found by a random search (that is, a system with an uniform probability of finding those objects).

    f) The Functionally Specified Information (FSI) in bits is simply –log2 of that number. Please, note that I imply no specific meaning of the word “information” here. We could call it any other way. What I mean is exactly what I have defined, and nothing more.

    One last step. FSI is a continuous numerical value, different for each function and system. But it is possible to categorize the concept in order to have a binary variable (yes/no) for each function in a system.

    So, we define a threshold (for some specific system of objects). Let’s say 30 bits. We compute different values of FSI for many different functions which can be conceived for the objects in that system. We say that those functions which have a value of FSI above the threshold we have chosen (for example, more than 30 bits) are complex. I will not discuss here how the threshold is chosen, because that is part of the application of these concepts to the design inference, which will be the object of another post.

    g) Functionally Specified Complex Information is therefore a binary property defined for a function in a system by a threshold. A function, in a specific system, can be “complex” (having FSI above the threshold). In that case, we say that the function implicates FSCI in that system, and if an object observed in that system implements that function we say that the object exhibits FSCI.

    h) Finally, if the function for which we use our objects is linked to a digital sequence which can be read in the object, we simply speak of digital FSCI: dFSCI.

    So, FSI is a subset of SI, and dFSI is a subset of FSI. Each of these can be expressed in categorical form (complex/non complex).

    I am fully available to discuss those definitions and their implications, if you are interested.

  201. 201
    EricMH says:

    @gpuccio, thank you very much! I will be reading this material in depth so I can understand the FI discussion.

    It is also interesting that both you and KF say DNA is a machine code. This seems obvious to me, too. I also read the same thing in Li and Vitanyi’s book on Kolmogorov Complexity. Yet, talking to the good doctors over at Peaceful Science they vehemently claim DNA is certainly not machine code.

    Once we grant DNA is essentially machine code, then the inference to design is also exceedingly obvious, at least for a programmer. We know full well we cannot create any sort of useful program by pumping random bits into a compiler, or even with a genetic algorithm or with genetic programming. The latter only are successful in highly constrained, carefully parameterized scenarios. GAs and GPs certainly do not work with a fully Turing complete language like the average programmer uses.

    So, I think that is why evolution proponents are so adamant that DNA is not machine code, although they cannot produce a coherent reason. For instance, we know DNA is Turing complete, hence the field of DNA computation.

    @Nonlin, can you setup a scenario of your choosing and apply your filter to the bitstrings? That would bring clarity to the discussion.

  202. 202
    daveS says:

    gpuccio,

    daveS at #188:

    “I would agree with this.”

    Well, as usual with Nonlin’s statements, I don’t agree at all!

    Both the Fibonacci series and the pi sequence that I have given at #150 are very good examples of meaningful and functional information.

    They are both meaningful because they both convey a specific mathematical meaning. They are, in that sense, universal mathematical objects. Therefore, they are descriptive information, exactly like a Shakespeare’s sonnet.

    But they are also, both of them, functional information (prescriptive information), because they can be used (both of them) in some empirical system to implement specific functions.

    Let me try to explain how I agree with what Nonlin posted.

    If I were walking on the street and a pedestrian suddenly shouted “Fibonacci sequence!” in my direction, then I don’t feel I would have received any information. Someone simply blurted out a proper noun.

    If the pedestrian had shouted “The 11th prime Fibonacci number is 2971215073!”, then I would have received some information.

    Likewise, when you tell me about all the interesting properties and structure the Fibonacci sequence has, as well as its many connections to various disciplines, that too conveys information.

  203. 203
    EricMH says:

    All, here’s another potentially useful concept.

    We’ve been remarking that FI is somewhere between extreme regularity and complete randomness. A quantity that captures this idea is the Kolmogorov minimal sufficient statistic (KMSS). It is a bit technical to define, but the important thing is that it is both incompressible and nonrandom, so it fits the inbetweenness of FI better than Kolmogorov complexity or Shannon information.

    An interesting property is KMSS is said to cleanly separate the signal and noise in an object.

    Another aspect is the KMSS is also self contained. It is defined without reference to an external context. It is a sort of idealized ASC.

  204. 204
    gpuccio says:

    daveS:

    I would like to discuss briefly (with you, not with him, because with him it’s hopeless) the wrong and ambiguous concept introduced by Nonlin that meaning, and I suppose function, is “user dependent”.

    That’s simply not true.

    Material objects exhibit properties that are objectively observed in them, even if those properties are i essentially abstract, even ifthose properties can be observed and understood only by some.

    That’s where Nonlin is wrong.

    A distant galaxy has a specific place in our sky, even if most people don’t know it, and cannot see it. And of course many people just don’t knoe what a galaxy is. Moreover, dogs and cats certainly don’t understand that.

    Does that make the galaxy less a galaxy? Its position less objective?

    I have previously mentioned speed. Speed is a property of objects, but it is certainly a very abstract concept. Cats don’t understand it. Not everybody could define it correctly. Certainly not cats and dogs.

    And yet, can we doubt that objects exhibit speed? hat we can measure it? That such a measure is very relevant to our models of reality?

    The same is true for information, in all its form.

    A string of symbols has an inherent potential information, that is easily computed as the number of a^n, where a is the number of possible symbols at each site and n is the number of sites.

    If the sequence is a working program in some computer language, it will have a dunctional information content: the ratio of the target space to the search space.

    Moreover, the sequence is of course embedded in some material object, as a specific configuration of the object. So, we are always dealing with material objects that exhibit some abstract property, like functional information.

    So, the specific Fibonacci sequence and the specific pi sequence that I gave has objective functional information, because they can be used by anyone who has the necessary understanding of what they are to implement specific functions.

    Even a watch has no meaning for cats and dogs. Does that make it less a wacth?

  205. 205
    EricMH says:

    @gpuccio, that’s right, I’ve noticed Nonlin saying information is subjective, which as you point out, is entirely incorrect. For example, the “unreasonable effectiveness of mathematics in the natural science” is the observer independent fact that there is great mutual information between the universe and mathematics (CSI), and thus excellent evidence the universe is intelligently designed. People, of course discovered it, but this doesn’t make the fact observer dependent anymore than Columbus discovering America caused America to pop into existence.

  206. 206
    daveS says:

    gpuccio,

    Yes, I don’t buy the “user dependent” part of Nonlin’s definition, so I agree with you on that point.

    The sentence “The area of a unit disk in Euclidean plane geometry is π.” expresses some information which objectively exists, and would exist even if no sentient being had discovered it.

    A string of symbols has an inherent potential information, that is easily computed as the number of a^n, where a is the number of possible symbols at each site and n is the number of sites.

    If the sequence is a working program in some computer language, it will have a functional information content: the ratio of the target space to the search space.

    I agree that if you describe the context fully, and tell me “the functional information content of this sequence is x”, then you have transmitted some information to me.

    Moreover, the sequence is of course embedded in some material object, as a specific configuration of the object. So, we are always dealing with material objects that exhibit some abstract property, like functional information.

    Perhaps it’s embedded in a material object, although I’m not sure that’s necessary. I could simply ponder the functional information content in a sequence which no one ever writes down, I suppose. Maybe we can just say at the moment we’re only interested in sequences which are realized physically?

    So, the specific Fibonacci sequence and the specific pi sequence that I gave has objective functional information, because they can be used by anyone who has the necessary understanding of what they are to implement specific functions.

    I don’t think I completely agree.

    You identified and posted this sequence and real number:

    0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377, 610, 987, 1597, 2584, 4181, 6765, 10946, 17711, 28657, 46368, 75025, 121393, 196418, 317811, 514229

    3.14159265358979323846264338327

    I don’t have much time right now, but I’ll ask a question: Does that representation of the first 30 digits of π tell you that this number is (approximately) the area of a unit disk in Euclidean plane geometry? I would say no, not directly. What happens is that you recognize that as an approximation to π and recall from other sources of information that π exactly equals the area of a unit disk.

  207. 207
    Mung says:

    EricMH:

    @Mung, here’s a quote from Papoulis, who wrote the book on random processes and variables.

    Is that from the following book?

    https://www.amazon.com/dp/0071226613

    Thanks!

  208. 208
    Mung says:

    daveS:

    For example, the sentence “The 11th prime Fibonacci number is 2971215073” does contain information. Do you agree?

    Sure. Now how do we quantify the amount of information in that sentence?

  209. 209
    Mung says:

    I am enjoying this conversation. Nice job guys!

  210. 210
    EricMH says:

    @Mung, yep that is the one. The quote is in one of the last chapters’ introduction where he is discussing the idea of entropy, which is the uncertainty of a set, with probability, which is the uncertainty of a specific event.

    And don’t miss my quote above from Li and Vitanyi, which also matches your interpretation of entropy.

  211. 211
    Mung says:

    EricMH:

    So, I think that is why evolution proponents are so adamant that DNA is not machine code, although they cannot produce a coherent reason. For instance, we know DNA is Turing complete, hence the field of DNA computation.

    Not only that, but they deny that the genetic code is a code!

    I avoid calling DNA a code, any kind of code. I don’t think it’s been shown that it is a code. The genetic code, otoh, meets the mathematical definition of a code.

  212. 212
    EricMH says:

    @Mung, what is the difference between DNA and the genetic code? I thought they are one and the same.

  213. 213
    EricMH says:

    A weird thing I’ve noticed is that people who disagree with ID also tend to be subjectivists. I saw this a whole lot when I was debating over at PS. Subjectivism seemed to be the premise underlying the main counter arguments I saw, such as the argument that entropy = information or that the LoING does not apply to the empirical realm.

  214. 214
    Mung says:

    gpuccio:

    Material objects exhibit properties that are objectively observed in them, even if those properties are i essentially abstract, even ifthose properties can be observed and understood only by some.

    Temperature, Volume, Pressure, Entropy, all come to mind.

  215. 215
    Mung says:

    EricMH:

    And don’t miss my quote above from Li and Vitanyi…

    That one is on order as well. 🙂

    So we will be able to look at the same page and the same forumalas. Unlike over at PS where they avoided texts on Information Theory and just asked me to take their word for it because they are experts.

    @Mung, what is the difference between DNA and the genetic code? I thought they are one and the same.

    The genetic code is a mapping. Like Morse code is a mapping. The genetic code maps a sequence of nucleotides to an amino acid. It’s how we get protein sequences from RNA sequences. The RNA sequences come from DNA sequences.

    What you want to look in biological terms are transcription and translation.

    Note that in the above process it is not the DNA that is the code. It is the mapping that is the code. And that is non-physical and abstract.

  216. 216
    gpuccio says:

    daveS:

    “Maybe we can just say at the moment we’re only interested in sequences which are realized physically?”

    Yes, for design detection that’s certainly the case.

    I agree with you: the only “place” where information can exist without being obviously “written” in a material substrate is in cosncious representations.

    “Does that representation of the first 30 digits of ? tell you that this number is (approximately) the area of a unit disk in Euclidean plane geometry? I would say no, not directly. What happens is that you recognize that as an approximation to ? and recall from other sources of information that ? exactly equals the area of a unit disk.”

    The point is: anyone (human or not human) who has understanding of the mathematical concepts of number, circle, circumference and diameter will know that there exists an important mathematical constant which expresses the ratio of circumference to diameter. And that such a constant has very peculiar mathematical properties.

    If that intelligent being can also recogniza numbers in base 10, it would be very easy to recogniza that the sequence is exactly that, the first 30 digits of that form of that constant.

    That information is universal, even if the specific form of expressing it is the form used in human mathematics.

    Mathematics is an universal language that requires only the understanding of its basic intuitions.

  217. 217
    gpuccio says:

    Mung:

    “Temperature, Volume, Pressure, Entropy, all come to mind.”

    Of course! 🙂

    And acceleration, position, momentum.

    Even mass, that would seem to be something more “material”, is indeed a very abstract concept: it can be defined in two competely different ways (inertial mass and gravitational mass), and that thy are the same thing is still only an assumption, even if verified by many measurements. Moreover, we know form relativity that mass is not a constant property of material bodies.

    All our scientific knowledge is essentially abstract, and yet it applies amazingly well to the physical reality. Information is no exception.

  218. 218
    Bob O'H says:

    Eric @ 177 –
    I see, so ASC isn’t CSI. I found one paper by Ewert et al. on ASC, but that just defines ASC. Is there a derivation of it somewhere? If it’s an objective property of external objects, then presumably is should be possible to show where it comes from.

    Similarly, you introduce a dependency term, and claim it solves the dependency problem, but I think you need the maths to back this up. The dependency issue crops up a lot in statistics in model selection, and there are many ways to approach it, depending on (amongst other things) what your intention is. So I think you need to be careful, and make sure you derive the correct measure.

  219. 219
    daveS says:

    Mung,

    Sure. Now how do we quantify the amount of information in that sentence?

    I have no idea how to do that step.

  220. 220
    gpuccio says:

    EricMH:

    “what is the difference between DNA and the genetic code? I thought they are one and the same.”

    Not exactly.

    DNA is a molecule made of nucleotides that realize long sequences.

    The genetic code is a symbolic way of reading those sequences, in protein coding genes and only in them, in “words” of three nucleotides each, representing AAs in the complex process of translation. The code is in base four (the nucleotides) and therefore a codon has 64 possible values, that cporrespond to the 20 aminoacids and to stop signals, in a specific, redundant way.

    The code is almost universal in living beings, but in principle other codes are possible.

    The interpetation of the code is linked to the complex machinery that implements translation (after transcription). The true components of that machinery that decript the code are the 20 aaRNA synthetases (or ligases), 20 vey big and very complex and very specific proteins that couple AAs to the corret tRNA.

    So no, DNA and the genetic code are not the same thing.

    By the way, DNA stores a lot of information of diffewrent type, that does not depende on the genetic code: for example in promoters, enhancers, and in many non protein coding genes that code for functional non coding RNAs.

  221. 221
    gpuccio says:

    EricMH:

    “A weird thing I’ve noticed is that people who disagree with ID also tend to be subjectivists.”

    How true!

    ID is definitely a very objective scientific paradigm, and its critics can give no real objective confutation of its ideas.

  222. 222
    Bob O'H says:

    Eric @ 209 – but probabilities are measures on sets. 🙂

  223. 223
    daveS says:

    gpuccio,

    The point is: anyone (human or not human) who has understanding of the mathematical concepts of number, circle, circumference and diameter will know that there exists an important mathematical constant which expresses the ratio of circumference to diameter. And that such a constant has very peculiar mathematical properties.

    If that intelligent being can also recogniza numbers in base 10, it would be very easy to recogniza that the sequence is exactly that, the first 30 digits of that form of that constant.

    That information is universal, even if the specific form of expressing it is the form used in human mathematics.

    Mathematics is an universal language that requires only the understanding of its basic intuitions.

    I agree with that much.

    But I wouldn’t expect that all that information about π is transmitted by the string “3.14159265358979323846264338327”.

    To those with sufficient background knowledge, that string is more or less a name for π. The shorter string “3.14” has essentially the same function (so perhaps it actually is compressible in that sense!)

    When we see it, we naturally think of interesting properties of π and connections to various fields, which are demonstrated elsewhere.

  224. 224
    EricMH says:

    @Bob O’H ASC is a more defined variant of CSI. I’m not quite sure what you are asking for. Are you wanting me to prove E[oCSI] <= 0?

    Those are Papoulis' words, not mine. Probability is of a specific event, entropy is of the probability distribution over a set of events.

  225. 225
    gpuccio says:

    daveS:

    The point is:

    We have someone who has to make an important computation, requiring the value of pi at 29 decimal precision.

    That person has not available those precise values of pi, and has not a program to compute them.

    A friend gives him a piece of paper where he has written the values.

    So the person can perform his computations.

    Of course, the piece of paper conveys functional information to the person. He can do something using it. That’s the point.

    Just think of it this way. Someone needs to use detailed values of pi, e and other mathematical constants for his daily work at his computer.

    So, he stores those values in a text file.

    Each time he needs a value, he opens the file, copies the needed value and pastes it in his computations.

    Can you deny that the text file has functional information?

    The same information can also be embedded in a program. In that way, no special intervention by people is necessary. the program uses the information in the variable “pi”, stored there as a 30 digit value, for its procedures and computations. Just as a cell uses the functional information in a protein coding gene to implement its activities.

    I cannot see any problem in all that.

  226. 226
    Bob O'H says:

    Eric @ 223 – For a start, it would be good to see a proof that your correction to CSI solves the dependency problem. It would also be nice to see a derivation of ASC, but I suppose that should have been Ewert’s job.

    Ironically, without any proofs ASC and your correction are just subjective choices of statistics.

  227. 227
    EricMH says:

    @Bob O’H The important property of ASC that Pr{ASC(X,P,C) >= a} <= 2^-a is proven in:

    https://robertmarks.org/REPRINTS/2013_OnTheImprobabilityOfAlgorithmicSpecifiedComplexity.pdf

    The solution to dependency follows from E[oCSI] <= 0. If the specification is dependent on the event, then all events have oCSI > 1, which means E[oCSI] > 0. So, contrapositive, if E[oCSI] <= 0, this means specification is independent of event.

  228. 228
    daveS says:

    gpuccio,

    Can you deny that the text file has functional information?

    No.

    Do you deny anything I have said above? I don’t think our positions are in conflict, really.

    Edit: In the scenario from #224, you speak of someone who simply needs a precise value of pi to substitute into a formula. Obviously that is exactly what the text file contains.

    But in #215, you mention a person who recognizes the contents of the text file as being a representation of pi, which has great import in geometry as well as other fields. That “background knowledge” about the amazing properties of pi is not contained in the text file.

    Are we in agreement about this?

  229. 229
    gpuccio says:

    daveS at #227:

    “I don’t think our positions are in conflict, really.”

    Neither do I. I think that we essentially agree. But I wanted to make very clear that I absolutely believe in the objective nature of the functional information embedded in an object, which can simply be summarized as follows:

    That object can really be used to implement the defined function.

    And the reason for that is that the object has the right configuration to ensure that.

    This is a fact, and there is nothing subjective in it.

    “In the scenario from #224, you speak of someone who simply needs a precise value of pi to substitute into a formula. Obviously that is exactly what the text file contains.”

    Yes.

    “But in #215, you mention a person who recognizes the contents of the text file as being a representation of pi, which has great import in geometry as well as other fields. That “background knowledge” about the amazing properties of pi is not contained in the text file.”

    Yes.

    “Are we in agreement about this?”

    Yes.

    The point is:

    Recognizing a function is one thing.

    Using an object to implement a function is another thing.

    Both things are part of the ID procedure. Both things depend in some measure on conscious interventions.

    That’s simply natural, because ID is about conscious interventions. Design is what we are trying to infer. And design is a conscious intervention.

    But in no way that implies that there is anything subjective in the procedure of measuring functional information and using it to infer design.

    I will try to be more clear.

    I am a conscious observer. I find a material object, and I want to decide if I can infer design for it.

    It’s not important who I am, or what I know, Because anyone can do the same things that I am doing, with different backgrounds and knowledge. Results will be different, in some cases. In most cases they will be similar.

    This is not important. Why?

    Because the purpose of the design inference is to infer design without false positives.

    It is not to infer design for all designed things.

    We happily accept that many false negatives will happen. We are not interested in that. We only want that, when design is inferred, it is not a false positive.

    IOWs, we are ready to trade as much sensitivity as necessary to get absolute specificity.

    This is important, and many do not understand it.

    That’s why nonlin writes, at #89:

    “Whoever tries to limit the search to known function, misses a lot of designs.”

    And so? Missing designs is not a problem. The purpose it to infer design correctly, when we infer it.

    So, let’s say that I have a Shakespeare sonnet and I am a non English speaking chinese, or a cat. I will not understand the meaning.

    And so? The worst scenario is that I don’t make a design inference and that will be for me a false negative. No problem there.

    But someone else, who understands the meaning, will make the right inference. And he will be right. No false positive.

    Of course, if I am a smart chinese. I could perhaps make a design inference for the sonnet just the same, because we know that some linguistic patterns can be recognized even if we don’t understand the meaning.

    For a cat, I don’t see big chances. 🙂

    The point is: recognizing a function requires a conscious observer who can understand the function, and define it. Not all conscious observers wil recognize a specific function. Maybe there are functions that no human conscious observer can really recognize. And so?

    A few more false negatives. No big problem.

    But the function is there. It is objectively there.

    If someone knows English language, he will understand the meaning of the sonnet.

    If someone understands the concept of measuring time, and can see that a watch can do exactly that, he will be able to use the watch to measure time.

    If someone needs the digits of pi, and in some way knows that the sequence written on that piece of paper is exactly that, he can use that sequence for his computations.

    That’s the part where we use the object to implement the function we have recognized and defined. That use is an empirical verification that the object can really be used to implement the function we have defined.

    Of course, the context for recognizing a meaning or a function, and therefore for using it and verifying that the object can really do what we think it can do, is always a context with conscious interventions and backgrounds. And so?

    As I have said, all science works that way.

    Nobody would ever recognize speed as a property of an object, if he were not a cosncious intelligent being. Least of all, could anyone who is not conscious (and not familiar with some mathematics) define instantaneous speed as the derivative of the change of position on time.

    And so? Is speed less objective for that? Of course not.

    Even when a program uses the pi sequence to make computations, and there is no conscious intervention in its working, the conscious intervention has been there before. The programmer of course understood the meaning of pi, and its functions.

    The program cannot exist without its programmer. But, in the same way, Newtonian mechanics would not exist without Newton (or without some other guy who could have done what Newton did).

    So, I think that we agree probably on all. But I want to be extremely clear about the objectivity of science, of information, of functional information, and of functional information in material objects.

    That’s all.

  230. 230
    DATCG says:

    Nonlin @89,

    Apologies for not responding before today.

    Before fully responding. To be sure I do not misunderstand you. Do you agree DNA is a Code? Do you agree there are multiple Codes of Life?

    Or, are you saying there is only Order?

    Thanks

  231. 231
    DATCG says:

    Upright Biped @110, Gpuccio@112

    Bipedal Buddy! How you doing? 🙂

    No my friend, this is not depressing. Depressing is being stuck in Venezuela, Cuba, or China, where one wrong word puts you in political prison or worse.

    At least here, the posters and readers can explore and debate to their hearts content – even if it does get old at times.

    Com’on now, tell us about Semiosis 😉 What is the difference between Semantics, programming functions, variables and Order? Or, Ordered patterns?

    Gpuccio covered it to a degree.

    You guys are all doing great btw. God Bless. Keep up the good work of exploring the failings of Darwinista Fairy Tales.

  232. 232
    DATCG says:

    Mung@119…

    Your suggestion led me to an old Sachmo tune, a “little light spiritual…”

    https://www.youtube.com/watch?v=SVKKRzemX_w

    ahhh Louis ohhhh yeaaah…

    Now someone tell me, how does a man smile so much while singing such a sad song 🙂

  233. 233
    Bob O'H says:

    Eric @ 226 – that’s not really helpful. I don’t want to see an elucidation of the properties, I want to see the derivation of ASC. Apparently it is something objective and not just pulled out of thin air (or from somewhere else), so there should be some maths to show that ASC is the correct formula for CSI (or whatever CSI is meant to estimate).

  234. 234
    kairosfocus says:

    EMH, when I have pointed to D/RNA as machine code using 4-state, prong-height elements, first, I spoke as someone who worked directly with such code in microprocessor/ microcontroller contexts. I am not arguing by analogy, I am recognising a very familiar pattern. We have, for protein synthesis, a start element. We have elongation by specific, stepwise end-directed process, add AA-X, add AA-y, etc. Then, there are the three halting codes. Halting, as is well known, is a major consideration relative to algorithms; stepwise successive finite procedures that carry out a given process to a definite end point. The existence of what, 20+ dialects shows that the meaning is set by a convention not force of necessity. Also, that the code is specific to the particular machine. And if one is hung up on most electronic computers being binary, 2-state, note that e.g. back in the ’50’s – 60’s the Russians built and used three-state machines; I actually have an interesting Russian textbook on the algebra of n-state discrete state (i.e. digital) entities. Of course, to physically execute instructions (prescriptive info) there will be associated execution machinery. Finally, machine language is an expression of language, here antecedent to cell-based life. Language is obviously a strong sign of a certain level of intelligence capable of verbal communication. There is very good reason to infer that cell based life expresses a computer architecture as part of an embedded system used to create the workhorse protein molecules. And yes, this is a design inference unfettered by a priori imposition of self-referentially incoherent evolutionary materialism (by way of so-called methodological naturalism or otherwise). KF

  235. 235
    kairosfocus says:

    BO’H:

    We measure length in feet, ells, yards, metres, chains, furlongs, miles [of different kinds] Angstrom units etc, there is no good reason why only one metric should ever be THE metric for a given quantity.

    For that matter, Info can be measured on base 2, base e and base 10 elements etc, using the same log-probability metric. It is enough that there be a reasonable metric, and as a statistician you will be familiar with the various kinds of scales, e.g. using the old NOIR mnemonic.

    If we can simply reasonably rank information and related quantities that can be enough to responsibly guide relevant decisions.

    In the relevant context, that FSCO/I is real (“objective”) and points to deeply isolated islands of function in large configuration spaces, simply ponder the pieces of an ABU 6500 C3 reel in a bucket. How many scattered configs are possible? How many arbitrarily clumped ones? Can we specify a string-based description language that gives the configs? Obviously, yes.

    Now, ponder the exploded parts assembly diagram. By comparison to the world of possible scattered or clumped configs, the set of functional ones is tiny, specific and constrained to an island of function. (There is significant tolerance, it isn’t just one possible config.)

    The requirement of well-matched, properly arranged components to attain relevant config-based function naturally leads to the island of function pattern.

    The description language approach then gives a natural metric based on string-length of Y/N q’s to specify a typical functional config, with due allowance for being efficient. Further, function can be independently described and recognised, i.e. we have targets.

    The point is reinforced by the description that entropy can be understood as typical missing info to specify microstate for an entity described at macro level to be in a macrostate. So, yes, there is a natural link between information and entropy, it is not just mathematical coincidence.

    We therefore have excellent reason to infer from observation of FSCO/I to design as credible, plausible, best empirically and analytically warranted explanation. For the search challenge for blind chance and/or necessity on gamut of sol system or observed cosmos becomes maximally implausible once we pass 500 – 1000 bits of info content. But as your own comments demonstrate, intelligently directed configuration — design — routinely creates such FSCO/I.

    If you wish to overthrow such, the proper answer is observed counter-example, not minutiae on how can you define or quantify beyond my ability to object or dismiss. The resort to the latter, which is now routine, tells us that the former has failed so often that hope has been given up.

    In short, design inference on functionally specific, complex organisation and/or associated information is well-supported.

    KF

  236. 236
    kairosfocus says:

    GP, re 203 and cats. Yesterday morning I saw a cat with three kittens. There being a mud puddle in the way, the cat walked up to it then jumped over the puddle. The kittens followed suit. I have some suspicions that cats and dogs are smarter than we may think. KF

  237. 237
    Bob O'H says:

    kf – if FSCO/I is real, then there should be some mathematics to show this. We’re not talking about something that is directly measurable, but it is calculated from some other observations. But nobody seems to be able to provide the maths to demonstrate why a particular calculation is made. What makes this worse is that there seem to be several possible calculations: CSI is not the same as ASC, which is not the same as what Eric is now suggesting, and I have no idea if any of these are the same as FSCI/O. It may be that CSI, ASC or FSCI/O is an objectively correct measure, but you have to demonstrate that: you can’t just declare it to be true.

  238. 238
    daveS says:

    gpuccio,

    Nobody would ever recognize speed as a property of an object, if he were not a cosncious intelligent being. Least of all, could anyone who is not conscious (and not familiar with some mathematics) define instantaneous speed as the derivative of the change of position on time.

    And so? Is speed less objective for that? Of course not.

    If there is or were such thing as absolute space, then speed would be an objective property of an object.

    Perhaps more relevant: If you tell me to calculate the speed of a particle relative to some reference frame, then there is an objectively correct value.

    Similarly, if you give me a well-defined procedure to calculate “functional information content” in a text file, say, then again, there is an objectively correct value.

    Whether that functional information is an objective property of the file, I’m less sure.

    Consider again the text file containing only the 30 digits of pi. I agree that in the context where an engineer needs that particular number, the text string is “functional” to her.

    But there are of course many other numbers that can be (approximately) represented using 30 decimal digits. Do the corresponding text files all contain functional information? I guess the engineer could be needing to use any of those ~10^30 different numbers at a given time, so it would seem so (perhaps there is some notion of user-dependence here). Does the file with the pi-string contain more functional information than most of the others?

    I don’t have a satisfactory answer to these questions, so I’m not sure the presence of functional information is an objective property of the text file (or its material realization in the computer itself).

  239. 239
    gpuccio says:

    kairosfocus:

    I love cats! I have three of them. 🙂

    They are very, very smart. No doubt about that.

    But even the smartest of my three, who is really smart! (she can open doors by jumping and grasping the handle, then making a very specific movement with her body) has not yet succeeded in appreciating Shakespeare’s sonnets!

    No problem. Maybe time will change that. Afetr all, many people don’t succeed in doing that, too. 🙂

  240. 240
    gpuccio says:

    Bob O’H:

    I cannot speak for others, but functional information as defined by me (which, I believe, corresponds well enough to the concepts expressed by KF) is an objectively correct measure.

    And it works perfectly fine to infer design.

  241. 241
    Bob O'H says:

    gpuccio @ 238 –

    But even the smartest of my three, who is really smart! (she can open doors by jumping and grasping the handle, then making a very specific movement with her body) has not yet succeeded in appreciating Shakespeare’s sonnets!

    This is a cat you’re writing about, so how would you know? 🙂

    gpuccio @ 239 – I can’t work out whether you’re joking or not.

  242. 242
    gpuccio says:

    daveS at #237:

    Good thoughts.

    Here are my counter-thoughts.

    The objectivity is in the object. The property we measure, of course, is different from the object, and is defined by compex contextx. But the point is that it can be objectively neasured in the object, given the context necessary for its measure.

    Speed is an objective property, but of course you have to give a context for its measure: for example, as you correctly say, a reference frame.

    If you change the reference frame, the measure will change. But it’s always the same property we are measuring. The specific measure depends on many things: the unit of measure, of course, and the context of the measure.

    You say:

    “Similarly, if you give me a well-defined procedure to calculate “functional information content” in a text file, say, then again, there is an objectively correct value.”

    Correct. I have done exactly that here:

    An attempt at computing dFSCI for English language

    https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/

    I do it for a Shakespeare sonnet.

    To be precise, I don’t compute a precise number for the functional information of the sonnet, but I reach a very reliable value for a higher threshold of the target space, and therefore for a lower threshold of the functional information. Which is about 800 bits. The real value is certainly much higher than that, but that value is alredy more than enough to infer design.

    You say:

    “Whether that functional information is an objective property of the file, I’m less sure.”

    It is an objective property (if explicitly defined) that can be objectively measured in the file. Is that good for you?

    “objective property of the file” is probably too philosophical. The above form is more correct.

    You say:

    “Consider again the text file containing only the 30 digits of pi. I agree that in the context where an engineer needs that particular number, the text string is “functional” to her.”

    OK.

    “But there are of course many other numbers that can be (approximately) represented using 30 decimal digits.”

    Of course.

    “Do the corresponding text files all contain functional information?”

    Almost everything contains some functional information. But almost all those numbers (and files) certainly do not contain any complex functional inforamtion.

    Just a simple example.

    I define a function:

    a) A number that can be set as the key for an electronic safe that requires a 30 digit number.

    That is a perfectly correct and explicit definition of a function.

    But any 30 digit number can implement that function.

    So, the ratio of the target space to the search space is 1.

    -log2 of 1 is:

    0 bits.

    With that function, functional information is 0. 0 is certainly lower than 500. So, there is no complex functional information.

    But let’s say that I define my function as follows:

    b) A number that can be set as the key for an electronic safe that requires a 30 digit number which does not include the digit “0”.

    This is a definition based on order. Not including the 0 is a form of order.

    So, here we can see well that order is a good way to specify, but we can also see the potential problem with that.

    Using the binomial distribution, and considering 0 as success, we can see that the probablilty of getting no zeroes in 30 attempts, with a probability of success for each attempt of 0.1, is:

    4.239116e-02

    So, if we have a 30 digit number that does not include 0, that number, for that defined function, will have a functional information of:

    4.56 bits

    Not much, but it is some functional information. However, certainly not complex functional information.

    In a random system, that type of number can reasonably be found.

    Now, let’s make it more difficult, always acting on order. let’s define a new function:

    c) A number that can be set as the key for an electronic safe that requires a 30 digit number which does not include any digit lower than “5”.

    Now, let’s use again the binomial distribution. The probabilty of success now is 0.5. So the probability for a result with 30 successes in 30 attempts by a random search is:

    9.313226e-10

    And the functional information for that function of a number that is part of the target space (IOWs, that does not include any digit under 5) is:

    30 bits

    OK, that’s not much, bt it is something. Let’s say, just to discuss, that we are considering a system with limited probabilistic resources, and that we have therefore set our threshold for complex functional information, for that system, at 25 bits. IOWs, in that system we have decided that it is reasonable to infer design if the object exhibits more than 25 bits of functional information.

    In that case, and for that system, we should infer design for a numbser that does not include any digit lower than 5.

    But… there is a problem. A problem that must always be considered when we specify by order.

    We must exclude necessity, which is always a possible explanation for order.

    IOWs, the above reasoning is correct, but only if in the system we are observing, at each attempt, the 10 possible digits are equiprobable, IOWs if each of thwm has a probability of 0.1.

    But let’s say that digits are randomly chosen in a system that can only generate 5 digits: 5 to 9.

    In that case, all the random results would be part of the target space, and again the functional information would be:

    0 bits

    and not:

    30 bits.

    IOWs, in that system there is a form of necessity that makes the target result necessaty in a random search.

    So, when we specify by order, we must always verify that in the system there is no necessity law that can explain the observed order.

    More in next post.

  243. 243
    gpuccio says:

    daveS at #237:

    Now, let’s see what happens when we specify by function. Let’s give a new definition for a 30 digit number.

    Let’s say that we have an electronic safe where a 30 digit key has already been set. But we don’t know it.

    So, the new definition is:

    d) A 30 digit number that can open this specific safe.

    This is a definition where the specification is purely functional. There is no reference to any specific property of the contingent sequence of digits. Nothing at all. And there is no reference to any order in the sequence. None at all.

    The only criterion is functional: will that number work as a key for this safe?

    We just need to use the number that we get from a random search, and see if it works or not.

    Let’s compute the target space and the functional information here.

    The target space is 1. The search space 1e30.

    So, the probability for the target space is:

    1e-30

    and the functional information for a number that opens the safe is:

    99.7 bits

    Now, that’s a good amount of functional information. It is not complex functional information in the general case of the whole universe (it’s lower than 500 bits), but I am sure that it would be more than enough to infer design in a lot of more limited systems, with lower probabilistic resources.

    Have we the same problem as before? Should we be exclude necessity?

    In principle, that is always true, but in practice that is not really a problem with functional specification.

    Why?

    Because if the key to the safe has been set randomly, no law of necessity in any system will be able to make it likely, without knowing the details of its contingent sequence.

    To have a necessity system I should:

    1) Know the key in advance

    2) Set a very special system where only the digits that are in the key can be selected

    IOWs, I should set up a fraud, something like Dawkin’s Weasel software. A context where the solution is already known.

    Another question: has order anything to do with the function?

    Of course not. Unless the person who set the key has deliberately chosen a very ordered sequence.

    But if the key was set randomly, the sequence will probaly have no special order. It may be slightly compressible, because any sequence can be. But not more or not less than most generic 30 digit random numbers.

    So, what I have tried to show is that:

    1) Functional information can be objectively measured in an object, given an explictly defined function, and for that function.

    2) In general, order has nothing to do with a functional specification.

    3) Functional specification has in general a great advantage vs specification by order or compressibility: it cannot in general be generated by any necessity law in the system. Necessity generates order, not function. The only exception being those few functions that are intentionally or naturally based on order.

    So, these are important points, IMO. And I have also tried to show in practice the procedures to measure functional information and to use it for a design inference.

  244. 244
    gpuccio says:

    Bob O’H at #240:

    No, I am not joking. Why would you think that?

    I am very serious.

    And I would appreciate your thoughts about that.

  245. 245
    gpuccio says:

    Bob O’H at #240:

    By the way, you may want to have a look at my comments #241 and #242. They are completely serious, I promise, in case you are wondering! 🙂

  246. 246
    ET says:

    Bob O’H:

    if FSCO/I is real, then there should be some mathematics to show this.

    You use it every day, Bob. For example computers wouldn’t exist without it. So clearly it is real. And clearly we can apply Shannon in order to measure it.

  247. 247
    Bob O'H says:

    gpuccio @ 243 – “I cannot speak for others, … as defined by me…” definitely mean you are being subjective.

  248. 248
    gpuccio says:

    Bob O’H at #246:

    I can’t work out whether you’re joking or not.

  249. 249
    Nonlin.org says:

    Gpuccio @197,

    You say:

    “The Fibonacci series that I have presented, for example, (30 numbers), can be used in practical contexts to implement many specific tasks, like the tiling of a surface or the drawing of a spiral. “

    So what? We can use everything to make something else. Does that mean everything is information?

    You say:

    “These two objects are good examples of the amazing truth, highlighted here by KF, that mathematical objects, while being in essence abstract”.

    Finally! Then you agree?

    Also, did you drop: “function is not order”? Here’s an example for you:
    Heart function = ordered EKG
    Heart function reduced = disordered EKG
    Heart doesn’t function = flat line EKG

    Conclusion, to identify function, we measure order. Always!
    But order also means necessity/design, so who needs the ‘function’ complication?

    Gpuccio @203,

    I didn’t say “function, is “user dependent” “. I said “information is user dependent”! Your misunderstanding explains your disagreement? Also, there’s a big distinction between function, objects, and information.

    EricMH @204,
    daveS @205,

    Math is not necessarily information. Information is what intelligent agents use to resolve uncertainty. And yes, sometimes we use math for that.

    Gpuccio @228,

    You write:

    “So, let’s say that I have a Shakespeare sonnet and I am a non English speaking chinese, or a cat. I will not understand the meaning.
    And so? The worst scenario is that I don’t make a design inference and that will be for me a false negative. No problem there.”

    This is wrong! We did infer design long before we understood cuneiform, hieroglyphs, etc. How? Because we observed order.
    And then you agree with me:

    “Of course, if I am a smart chinese. I could perhaps make a design inference for the sonnet just the same, because we know that some linguistic patterns can be recognized even if we don’t understand the meaning.”

    And then you still disagree? Will you make up your mind?

  250. 250
    gpuccio says:

    Nonlin.org:

    Yes, I still disagree. Period.

  251. 251
    daveS says:

    gpuccio,

    I would agree that if we consider the entire system of the particular safe together with a text file containing the correct key, then it makes sense to say the text file contains functional information in that context.

    So we talk about functional information of a system of interacting “parts”, so to speak?

  252. 252
    Nonlin.org says:

    EricMH @200

    You ask: “can you setup a scenario of your choosing and apply your filter to the bitstrings? That would bring clarity to the discussion.”

    It’s very simple, really. We NEVER-EVER have to analyze sequences like you asked:
    “1. HHHHHHHHHHHHHHHHHHHH
    2. HTHHTTTHHTTTTTHTTTTT
    3. THHTHHHTTHTHHHTHHHHT”

    Instead, we’re dealing with patterns that go on and on and on. Take galaxy shape (trillions of them?), take sand dunes waves (trillions?). Take shape of DNA segments (trillions?). And of course DNA is in every cell of every organism out there. We can take DNA and see several non-random features: nucleotides type, shape of the DNA chain, DNA conservation over organism types, etc.

    Let’s pick one of these, ‘nucleotide type’, and reject the null hypothesis: “DNA is a random composition of A, C, G, T, and X (at least one more) nucleotides”. Select a DNA segment of say 100 nucleotides and see P( “no X encountered” | null) = (4/5)^100 = 2.03704E-10 which is way lower than the typical .05 threshold. Conclusion: “reject null”, therefore unlikely for this DNA to contain a nucleotide other than ACGT making ‘nucleotide type’ “not random”.

    Of course, we only looked at one 100 nucleotide-long sample. Feel free to extend this analysis to the whole population of such samples. For political polling, I believe they select 1000 samples from the whole US population. But for every one of those extra sample showing the same pattern, the Null becomes even more unlikely.

    Next, can we identify a designer of this feature? No! Then ACGT composition is a DNA “necessity”.

    But “Necessity is Design to the best of our knowledge”:
    http://nonlin.org/intelligent-design/
    Final conclusion, ‘nucleotide type’ is a designed feature. Simple.

  253. 253
    Nonlin.org says:

    DATCG @229,

    Yes, DNA seems to be Code. Yes, there seem to be multiple Codes of Life.

    Regarding Order, I say that Order is all we need to infer Design. We don’t need to prove ‘Function’ and we don’t need to prove ‘Code’.

  254. 254
    gpuccio says:

    daveS:

    “So we talk about functional information of a system of interacting “parts”, so to speak?”

    We talk about functional information in a system, if we are talking of one specific object.

    Functional information in an object is always measure for a specific, explicitly defined, function and in a specific, explicitly defined, system.

    The system is of fundamental importance, because:

    a) It defines what the object can do (it is the context where function takes place)

    b) It defines the probabilistic resources that could generate information by a random search or walk, both in terms of number of events in a time unit and of time span.

    We can never consider the functional information of an object in an abstract setting, or for an undefined function. That is a very important point.

    For example, an enzyme can certainly catalyze some important biochemical reaction, but only if it is in the right cellular environment. It could not survive out of it.

    Some parts of the environment are necessary to just allow the existence and survival of the object. Other parts are implied in the function itself. For example, in the case of the enzyme, substrates must be present, and they are involved in the function itself.

    But we compute functional information for one object, and for a function that is explicitly defined, and of course includes the right context, if we want to be fastidious. So, if we define the function for one enzyme, we will include what it can do, at what minimal level of efficiency, and in what context (including the presence of substrates). Then, and only then, we can verify the function and compute the functional information.

    Of course, our “object” can be an individual object, or a set of objects. It can be an enzyme or an enzyme cascade. In general, if we compute the functional information for a set of objects, it is important that they represent an irreducibly complex set. Then the FI of each object must be added to get the FI of the whole set (IOWs the probabilities multiply).

    Let’s go back to my example of the safe.

    If our interest is in the emergence of the key in the system, then we focus on the key. Let’s say that we know that the safe was already there, with its combination already set, and then in some way an object emerges in the system that can work as a key.

    Our question is if the emergence of the new object can be explained by a random search. Therefore we focus on the observed key, and we compute its functional information, given the safe.

    Each time that a new protein emerges in natural history, and can do something new, it requires of course an existing cellular backgorund for the new function to be possible. But we take that as already being part of the system.

    We focus on the new functionality of teh new protein, in the existing environment. That’s the function for which we compute functional information, to undesratnd if the emergence of the new protein can be explaine by a random search or walk.

    So, the functional information we measure is always for a well defined object, which in some cases can be a set of objects, and refers to that object or set of objects, given all the rest that is necessary for the function to be implemented.

  255. 255
    daveS says:

    gpuccio,

    We can never consider the functional information of an object in an abstract setting, or for an undefined function. That is a very important point.

    I see. Let’s say we have a key and two locks, L1 and L2.

    Assume the key fits L1 but not L2.

    Then in the system {key, L1}, the key probably contains a great deal of functional information.

    In the system {key, L2}, the key has little or no functional information.

  256. 256
    gpuccio says:

    daveS:

    Yes, if a numeric key exists in a system where it cannot open anything, of course it has no functional information in that system.

    It is equivalent to any random numeric key that cannot do anything in the context where it arises. So, we have no reason to infer design for it. Why should a designer design a numeric key that cannot open any lock in its context?

    So, what is your point?

  257. 257
    daveS says:

    gpuccio,

    No “point”, just making sure I understand!

  258. 258
    gpuccio says:

    daveS:

    OK, that’s fine.

    Please, feel free to ask anything you like, and I will try to answer.

  259. 259
    kairosfocus says:

    BO’H:

    With all due respect, over many years now we have routinely provided values, formulae and even tabulated results from the literature.

    You have been here all along.

    So, your dismissal by pretence that no quantitative results exist — that is implied by your language in : ” if FSCO/I is real, then there should be some mathematics to show this . . . But nobody seems to be able to provide the maths to demonstrate why a particular calculation is made” — simply tells us that your objection is sustained in the teeth of evidence. This is rather like the common “there is no evidence” objection of too many who through exerting selective hyperskepticism in fact are only dismissing evidence that is on the table that they do not wish to acknowledge.

    I will simply cite a simple model I put up as part of a discussion not far short of a decade ago, where the idea is to find an information value, use a dummy variable to reflect functional specificity and use a threshold (500 or 1000 bits). This in fact is linked to the sort of metric put up many years ago in quantitatively defining CSI, through log manipulation. Logs, being key to information metrics.

    Here we go:

    chi is a metric of bits from a zone of interest, beyond a threshold of “sufficient complexity to not plausibly be the result of chance,” (398 + K2). So,

    (a) since (398 + K2) tends to at most 500 bits on the gamut of our solar system [[our practical universe, for chemical interactions! ( . . . if you want , 1,000 bits would be a limit for the observable cosmos)] and

    (b) as we can define and introduce a dummy variable for specificity, S, where

    (c) S = 1 or 0 according as the observed configuration, E, is on objective analysis specific to a narrow and independently describable zone of interest, T:

    Chi = Ip*S – 500, in bits beyond a “complex enough” threshold

    NB: If S = 0, this locks us at Chi = – 500; and, if Ip is less than 500 bits, Chi will be negative even if S is positive.

    E.g.: a string of 501 coins tossed at random will have S = 0, but if the coins are arranged to spell out a message in English using the ASCII code [[notice independent specification of a narrow zone of possible configurations, T], Chi will — unsurprisingly — be positive.

    Following the logic of the per aspect necessity vs chance vs design causal factor explanatory filter, the default value of S is 0, i.e. it is assumed that blind chance and/or mechanical necessity are adequate to explain a phenomenon of interest.

    S goes to 1 when we have objective grounds — to be explained case by case — to assign that value.

    That is, we need to justify why we think the observed cases E come from a narrow zone of interest, T, that is independently describable, not just a list of members E1, E2, E3 . . . ; in short, we must have a reasonable criterion that allows us to build or recognise cases Ei from T, without resorting to an arbitrary list.

    A string at random is a list with one member, but if we pick it as a password, it is now a zone with one member. (Where also, a lottery, is a sort of inverse password game where we pay for the privilege; and where the complexity has to be carefully managed to make it winnable. )

    An obvious example of such a zone T, is code symbol strings of a given length that work in a programme or communicate meaningful statements in a language based on its grammar, vocabulary etc. This paragraph is a case in point, which can be contrasted with typical random strings ( . . . 68gsdesnmyw . . . ) or repetitive ones ( . . . ftftftft . . . ); where we can also see by this case how such a case can enfold random and repetitive sub-strings.

    Arguably — and of course this is hotly disputed — DNA protein and regulatory codes are another. Design theorists argue that the only observed adequate cause for such is a process of intelligently directed configuration, i.e. of design, so we are justified in taking such a case as a reliable sign of such a cause having been at work. (Thus, the sign then counts as evidence pointing to a perhaps otherwise unknown designer having been at work.)

    So also, to overthrow the design inference, a valid counter example would be needed, a case where blind mechanical necessity and/or blind chance produces such functionally specific, complex information. (Points xiv – xvi above outline why that will be hard indeed to come up with. There are literally billions of cases where FSCI is observed to come from design.)

    xxii: So, we have some reason to suggest that if something, E, is based on specific information describable in a way that does not just quote E and requires at least 500 specific bits to store the specific information, then the most reasonable explanation for the cause of E is that it was designed. The metric may be directly applied to biological cases:

    Using Durston’s Fits values — functionally specific bits — from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:

    RecA: 242 AA, 832 fits, Chi: 332 bits beyond
    SecY: 342 AA, 688 fits, Chi: 188 bits beyond
    Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond

    Compressibility, in this context, is one way of estimating informational content. The exchanges above on citing strings of digits of pi etc by using a generating algorithm actually illustrate the point. Pi is a property of nature, an irrational. This defines a target zone, here, a string that equals pi to a suitably large number of digits.

    Let us say, a quasar is cycling through pi to 10,000 binary digits. Is this chance and/or necessity or an intelligent signal? (And BTW, I here allude to the point that at the heart of information and communication theory is the inference on FSCO/I to signal, not noise. This is exemplified by the function of signal to noise ratio.)

    The issue here, is that the information metric of pi to 10,000 binary digits is expressible in an algorithm capable of generating it. Such an algorithm will readily exceed 128 – 256 bytes, and it is not plausible that a solar system or the observed cosmos as a whole would blindly generate an entity that transmits pi to such precision in some reasonable binary code. But, as a Quasar is a cosmos-scale effective transmitter, it is plausible that a civilisation wishing to announce its presence could perhaps find a way to modulate a quasar to transmit pi.

    So, even without knowing how that could be done, detecting such a candidate signal would directly lead to the inference, signal, not noise.

    And of course, digits of pi in a CODE reflect language, a characteristic of intelligence.

    Indeed, the presence of language implies presence of a complex system of communication which points to a huge body of organised information and knowledge. So, there is actually a LOT of information in such a signal, beyond the explicit one of 10,000 digits of pi. This is a point UB has repeatedly put on the table, for cause.

    Going to a more relevant case, in cell based life forms, we find a digital, 4-state alphanumeric code of undeniably very large complexity and high information content. It is part of a wider cybernetic system embedded in the core life functions of a metabolising, self-replicating automaton. Proteins are informational polymers, assembled algorithmically, with information that is patently functionally specific, complex, coded, based on specific configuration, organised into a functional entity and obviously information-bearing.

    We have found message, not noise, under the microscope not through a radio telescope.

    The clear import is, that cell-based life is an artifact, a product of design based on sophisticated technology several generations beyond our current stage with Venter et al.

    That is plain, and it would be amusing to observe the intellectual gymnastics used to obscure the plain message — if it were not in the end such a sad indictment of the condition of our civilisation’s intellectual culture.

    What we need to explore going forward is why we are so resistant to what is patent.

    KF

  260. 260
    kairosfocus says:

    DS, a lock and a key convey a huge body of functionally specific coherent information [start with, exploded views and the technological and societal context of locks and keys], even if a given key does not fit a particular lock. This of course extends to the living cell, which uses key-lock fitting complex functional elements. To point to a similar case, a gear — even in isolation — conveys a huge body of information. Including BTW that it necessarily embodies a fairly precise estimate of pi, once it is circular. The radius and circumference connected to an integral number of evenly spaced teeth with a common shape guarantees that, given the underlying geometry. KF

  261. 261
    kairosfocus says:

    GP, cats appreciate people who appreciate poetry. Especially if they also provide milk! KF

  262. 262
    kairosfocus says:

    ET, yes. It is almost amusing to see people using technology pivoting on functionally specific complex organised information systems to deny the import of such technologies and systems. Then, look in the living cell which has such in it, only, it has gone on to be metabolic and a von Neumann kinematic self replicating entity. Paley’s ghost is laughing. KF

  263. 263
    gpuccio says:

    KF:

    Or, like in my case, also delicious and expensive cat-food! 🙂

  264. 264
    EugeneS says:

    Nonlin

    “Entropy is a property of data”

    Nothing to do with data.

    Entropy is a function of state of a thermodynamic system provided the given system can be described as a thermodynamic one, which is not always the case.

    In the Russian textbooks, the latter condition is labelled as the “0-th law”, which simply assumes the existence of temperature as an adequate function of state. E.g. our universe as a whole is not a thermodynamic system. This is because of gravity that essentially renders temperature inadequate for it as a whole. However, parts of our universe, big and small, can be adequately described as thermodynamic systems.

    Information as it is defined in textbooks is related to entropy and is therefore also a function of state. It is the amount of surprisal an observer gets when s/he observes a system state.

    Functional information as defined in ID is a similar concept requiring an additional specification of a function in a properly defined context.

  265. 265
    daveS says:

    gpuccio,

    Please, feel free to ask anything you like, and I will try to answer.

    Thanks, I’ve never looked carefully at threads on functional information, so it takes me a while to grok the concept. The key/lock example clears things up a great deal.

  266. 266
    gpuccio says:

    EugeneS:

    Thank you for the important information. 🙂

  267. 267
    gpuccio says:

    daveS:

    I am happy that you are considering the concept. 🙂

    As you seem to like safes, you could be interested in another example where I have used the. It is a mental experiment that I have used with Joe Felsestein. I paste it here form a comment of mine in another thread:

    Of course. The key concept is always the complexity that is necessary to implement the function.

    A very interesting example to understand better the importance of the functional complexity of a sequence, and why complexity is not additive, can be foun in the Ubiquitin thread, in my discussion with Joe Felsestein, from whom we are waiting for some more detailed answer. It’s the thief scenario.

    See here:

    The Ubiquitin System: Functional Complexity and Semiosis joined together.

    https://uncommondescent.com/intelligent-design/the-ubiquitin-system-functional-complexity-and-semiosis-joined-together/#comment-656365

    #823, #831, #859, #882, #919

    I paste here, for convenience, the final summary of the mental experiment, from comment #919 (to Joe Felsestein):

    The thief mental experiment can be found as a first draft at my comment #823, quoted again at #831, and then repeated at #847 (to Allan Keith) in a more articulated form.

    In essence, we compare two systems. One is made of one single object (a big safe). the other of 150 smaller safes.

    The sum in the big safe is the same as the sums in the 150 smaller safes put togethjer. that ensures that both systems, if solved, increase the fitness of the thief in the same measure.

    Let’s say that our functional objects, in each system, are:

    a) a single piece of card with the 150 figures of the key to the big safe

    b) 150 pieces of card, each containing the one figure key to one of the small safes (correctly labeled, so that the thief can use them directly).

    Now, if the thief owns the functional objects, he can easily get the sum, both in the big safe and in the small safes.

    But our model is that the keys are not known to the thief, so we want to compute the probability of getting to them in the two different scenarios by a random search.

    So, in the first scenario, the thief tries the 10^150 possible solutions, until he finds the right one.

    In the second scenario, he tries the ten possible solutions for the first safe, opens it, then passes to the second, and so on.

    A more detailed analysis of the time needed in each scenario can be found in my comment #847.

    So, I would really appreciate if you could answer this simple question:

    Do you think that the two scenarios are equivalent?

    What should the thief do, according to your views?

    This is meant as an explicit answer to your statement mentioned before:

    “That counts up changes anywhere in the genome, as long as they contribute to the fitness, and it counts up whatever successive changes occur.”

    The system with the 150 safes corresponds to the idea of a function that include changes “anywhere in the genome, as long as they contribute to the fitness”.

    The system with one big safe corresponds to my idea of one single object (or IC system of objects) where the function (opening the safe) is not present unless 500 specific bits are present.

  268. 268
    Antonin says:

    DaveS:

    The key/lock example clears things up a great deal.

    It’s a very misleading analogy for biological systems. I see why gpuccio would like it as it closely aligns with the idea of tiny islands of function rising like needles from a vast sea empty of function.

    Chemical interaction is not all or nothing. ATP affinity, for example, is a variable depending on binding energy. A safe key either opens the safe or doesn’t. In biology, a primitive function can be subject to improvement by selection. You can’t evolve a key by trying different ones – you get just zero or one! Which is why keys, locks and islands of function seem to be preferred analogies here. Choosing your analogy on the basis of disproving evolution is reassuring if you are ideologically opposed to a concept but risks being dismissed as straw-man building. 🙂

  269. 269
    daveS says:

    gpuccio,

    What should the thief do, according to your views?

    Turn away from a life of crime, of course! 😛

    Thanks, that is a very clear illustration.

  270. 270
    daveS says:

    Antonin,

    I don’t know anything about biology, and unfortunately that’s not going to change. I’ll take the key/lock example literally rather than metaphorically.

  271. 271
    Antonin says:

    DaveS:

    I don’t know anything about biology, and unfortunately that’s not going to change. I’ll take the key/lock example literally rather than metaphorically.

    Fair enough. It’s not going to be any help to you in understanding evolutionary biology, though. Evolution works by reiterations of small changes (that are heritable) either accumulating or being lost from a population of organisms. None of this is remotely like a key and lock.

  272. 272
    Bob O'H says:

    kf @ 258 – you don’t understand what I’m asking for. I’m asking for some mathematics as would be understood by mathematicians (i.e. proofs, lemma, modelling etc), not simply plugging numbers into formulae. I think Eric would understand this, but I appreciate that mathematics carried out by professional mathematicians is very different to what the general public think it is (i.e. what they are exposed to in school).

  273. 273
    EricMH says:

    @Bob O’H ASC is an objective property of an object insofar as probability and Kolmogorov complexity are objective properties.

    First, a point of clarification, ASC is essentially a kind of hypothesis test. This is important because the probability used in the ASC is not the actual probability of the object occurring, but the probability with reference to a specific chance hypothesis, and this relative probability has an objective definition. The idea is that if ASC is high enough, then the chance hypothesis is not a valid explanation for the object.

    Kolmogorov complexity is objective due to the invariance theorem, which says one Turing machine can be translated into another with a constant size program, so the Kolmogorov complexity of a bitstring will only vary by up to this constant amount when comparing across two different Turing machines.

  274. 274
    EricMH says:

    @Nonlin, it seems your definition of random is “no limit on possible outcomes.” You are probably aware that if we have an infinite number of objects with a uniform distribution, then each object has a 1/infinity = zero probability of occurring. With your definition of randomness, then the fact that something exists rather than nothing is considered order and thus intelligent design. Is this what you mean?

  275. 275
    kairosfocus says:

    BO’H: with all due respect, condescending to a med doctor with strong math-stats and physicists with relevant math does not even begin to work; I just note to you that axiomatic math systems, theorems, lemmas etc are familiar to anyone who has done old fashioned Geometry much les uni math course sequences; they do not change the facts at work. If you want, we simply need metric models and those are on the table, long since. It is also distractive, given that Durston et al and others are an easy search away — besides, WP comboxes don’t readily support symbols or insertion of images or vids, at least here at UD as is understandable. A glance at Shannon’s paper will show the very well established baseline that alternative configs are information-bearing but that is commonplace: on/off or y/n or t/f or hi/lo state systems are all around. The D/RNA system is known to be a 4-state coded entity for synthesising proteins which work on in the main a 20-state system. The refinements from 2 bits per base or 4.32 bits per AA have to deal with redundancies etc. That we require 100’s of proteins in a minimal cell, that average length is about 300 AA per protein, are all notorious. Average 1 bit per AA as a generous estimate, 500 proteins, 200 AA/protein, we are looking at 200 x 500 x 1 = 100,000 bits to account for for a baseline cell. Every bit beyond 1,000 doubles the config space from 1.07 * 10^301. The observed cosmos of 10^80 atoms, with 10^12 – 15 atomic state interactions per s, cannot even scratch the surface of that sort of config space. Blind needle in haystack search is just not plausible as Abel long since showed, a result linked in your presence any number of times. Even this is distractive, the key thing is we see complex code that indicates language systems antecedent to cell based life; a matter of huge complexity. The design inference on indicated FSCO/I could not be plainer. You would do better to refer to Orgel’s 1973 work and at least acknowledge what he did frankly from the outset, actually effectively framing the descriptive terms I just abbreviated. The take-away I have is that a failed ideology tracing to decades before info systems were found in the heart of cell based life is being propped up. KF

  276. 276
    kairosfocus says:

    Antonin, the molecular scale key-lock systems have to do with proteins etc, D/RNA and the like composing the nano-machines of the cell. Think about the double-helix. Do you recall how sickle-cell trait works to block malaria? KF

  277. 277
    gpuccio says:

    daveS and Antonin:

    Of course the example of the key is very simple, and it has a target space of 1, which maked the discussion simpler. But its purpose is only to clarify the concepts about functional information, not to be a simulation of biological environments.

    So the mental experiment of the thief has one specific purpose: to clarify that functional information is not additive, but multiplicative, and that the idea of fitness advantages spread out in the system is not good at all to explain true functional complexity. That was a specific answer to a wrong statement by Joe Felsestein, that I have quoted, and I am not aware, as far as i can know, that he has answered my point.

    Antonin, what you say at #267 is simply not true. While I am the first to defend the point that NS can do something in the biological world, and as you can see even in this thread I really have to defend that idea with some of my ID friends here, I have also analyzed in depth what NS can and cannot do, according to the facts we have.

    I have also quoted to you my OP about that point:

    What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/

    If I remeber well, at some point you have gone away from that discussion, saying that you did not know biology well enough to discuss my specific arguments, and that others, like Joe Felsestein, could do that better.

    So, it’s really strange that now you come again into the discussion to warn daveS, who very candidly admits that he understands nothing of biology, that it could be “misleading” for him to follow my reasonings.

    So, what is it? Do you understand enough of biology to advice others? But not enough to discuss my biologic arguments?

    Do you know that old, and very wise, saying?

    “A little knowledge is a very dangerous thing”.

  278. 278
    Antonin says:

    A little learning is a dangerous thing;
    drink deep, or taste not the Pierian spring:
    there shallow draughts intoxicate the brain,
    and drinking largely sobers us again.

    Alexander Pope

  279. 279
    Antonin says:

    If I remember well, at some point you have gone away from that discussion, saying that you did not know biology well enough to discuss my specific arguments, and that others, like Joe Felsestein, could do that better.

    Professor Felsenstein is a geneticist, specializing in population genetics, a mathematical approach to allele distribution. Of course he’s going to be able to more eloquently point out the flaws in your approach. Maybe somebody who reads this site and also reads The Skeptical Zone could remind him of your latest comments.

    So, it’s really strange that now you come again into the discussion to warn daveS, who very candidly admits that he understands nothing of biology, that it could be “misleading” for him to follow my reasonings.

    I was surprised by Daves saying he didn”t think he would ever understand biology, as the principal mechanism of evolution is, in my view, very straightforward. And, I repeat, the lock/key analogy is misleading for the very reason you state. There is no prize for a near miss. In biology, life’s diversity demonstrates there are many solutions to finding a living.

    So, what is it? Do you understand enough of biology to advice others? But not enough to discuss my biologic arguments?

    As I’ve said, I don’t think your approach is persuasive. I don’t think it is an accurate model of reality.

  280. 280
    kairosfocus says:

    Antonin, the issue still lies on the table, un-addressed by you. Sad, really. Maybe, another day we can actually look at it? As in, start from code — alphanumeric code — in the heart of the functionality of the living cell, thus language and things intelligent beings do with it such as algorithms. KF

  281. 281
    Antonin says:

    Antonin, the molecular scale key-lock systems have to do with proteins etc, D/RNA and the like composing the nano-machines of the cell.

    Indeed. Chemistry, not computer programs. Mathematical modelling is all very well if your model reflects reality. Saying the model disproves reality assumes the model is accurate, is effectively begging the question.

    Think about the double-helix.

    There, the model was accurate (finally, after Rosalind Franklin gave Crick and Watson the hint about water molecules)

    Do you recall how sickle-cell trait works to block malaria?

    Are you referring to the benefit incurred from being heterozygous in an area infested with malaria?

  282. 282
    Antonin says:

    Antonin, the issue still lies on the table, un-addressed by you.

    Which issue? I am not the fount of all wisdom, just some random guy on the internet. But then, so are you

    Sad, really. Maybe, another day we can actually look at it?

    Is the answer computer models such as algorithms?

    As in, start from code — alphanumeric code — in the heart of the functionality of the living cell, thus language and things intelligent beings do with it such as algorithms.

    I think one should first observe reality – then try to model it. You have it backwards.

  283. 283
    kairosfocus says:

    Antonin, the chemistry is a means to effect the information system. The chaining in the strand of D/RNA is just that, chaining that does not drive the succession of AGCT/U. It is in that succession that the code for a given protein appears; as anyone with even school science now knows. A point highlighted by Crick, for example in his March 19, 1953 letter to Michael. That code, as Nobel prize work showed 50+ years past, is the basis for coding the assembly of protein chains, which then fold and are agglomerated to form the functional machinery of cell based life. We are seeing, start and put down methionine, elongate with a specific succession of AA’s (which then folds and fits to function) then stop, halt (an important feature of algorithms). None of this is now strange or dubious; 1953 was 65 years ago. I simply point out that this is machine level code in action, a familiar thing. Codes based on strings, an equally familiar data structure; and yes, this is at a conceptual level above the physical-chemical interaction — a familiar phenomenon with layercake architecture information systems. We are looking at language and information systems at work in the living cell, a world of deep complexity well beyond just the particular messages. It is therefore interesting and telling in the end to observe the rhetoric of distancing, dismissing and distraction. KF

  284. 284
    kairosfocus says:

    Antonin, again. I wrote in reply to your irrelevant citation of Pope to dismiss someone who has knowledge you would be well advised to at least attend to. As you see I then followed up on the dismissive remark that in the first instance pivoted on a reference to Chemistry. Again, you are revealing a rhetorical pattern which is instructive and at least does the service of showing us the thought patterns involved. KF

  285. 285
    Antonin says:

    I simply point out that this is machine level code in action

    Well, that’s an analogy.

  286. 286
    Antonin says:

    I wrote in reply to your irrelevant citation of Pope

    Did you miss that gpuccio cited him first, presumably with the same intent you attribute to me?

  287. 287
    kairosfocus says:

    Antonin, you are exchanging messages with someone who used to read Machine code in hexadecimal form. Tossing out the rhetorical grenade “analogy” does not cut it as a sound reply. The genetic code is a code, and it is used in a step by step finite sequence that is machine-dependent (20+ dialects) and creates protein strings. KF

    PS: I saw your citation in response to a serious discussion. On evidence in hand, GP — for years — has shown the depth of knowledge to point to need for such. What you have done above does not pass that bar. (Reminds me of some questions I asked Alexa today while waiting to pay a bill.)

  288. 288
    Antonin says:

    That code, as Nobel prize work showed 50+ years past, is the basis for coding the assembly of protein chains, which then fold and are agglomerated to form the functional machinery of cell based life. We are seeing, start and put down methionine, elongate with a specific succession of AA’s (which then folds and fits to function) then stop, halt (an important feature of algorithms).

    Yet in the chemistry, there are echos of precursors. The code is not quite universal and there is redundancy. Just a few less amino acids in the mix and you only need a doublet code. Keep things simpler, use your genetic storage also as a catalyst. Of course clunkier, less efficient organisms get drowned out in the struggle for life. Ignoring evolutionary possibilities, what we see now is how it has always been, is (sorry, gpuccio) the approach of the Texas Sharpshooter!

  289. 289
    Antonin says:

    Antonin, you are exchanging messages with someone who used to read Machine code in hexadecimal form.

    That would explain why poor computer analogies appeal to you. 😉

  290. 290
    kairosfocus says:

    PPS: I should perhaps remark briefly on analogies i/l/o the modern understanding of induction as arguments of support rather than demonstration. Many analogies are instructive and indeed supportive. It is not good enough to just toss such out dismissively. Where also, genus-difference and common characteristics are relevant considerations. In fact, 6809 machine code differs from DNA protein assembly code, and they work on different machines using different computational substrates. They have a different state system, 2 vs 4 for elements. None of that changes how we are dealing with string data structures, prescriptive language, algorithms with initiation, step by step processing and halting, or the common point that algorithms are inherently goal-directed. Language appears in the heart of the living cell, integral to its operations.

  291. 291
    Antonin says:

    KF, when you, Eric, gpuccio, anyone who thinks ID has some usefulness as an approach in understanding biological systems, can tell the difference between DNA sequences that have some biological activity from those that don’t, without synthesizing them, then I’ll revise my view on ID.

  292. 292
    ET says:

    Antonin:

    Yet in the chemistry, there are echos of precursors.

    No, there are just hints of intelligence, as in the code is fashioned in a specific manner that the anti-IDists think echoes of chemical precursors.

  293. 293
    ET says:

    Antonin:

    Professor Felsenstein is a geneticist, specializing in population genetics, a mathematical approach to allele distribution. Of course he’s going to be able to more eloquently point out the flaws in your approach.

    Everything he says about ID is flawed. Even a layperson can point out the obvious flaws in Felsenstein’s criticisms of ID.

  294. 294
    Antonin says:

    ET:

    No, there are just hints of intelligence, as in the code is fashioned in a specific manner that the anti-IDists think echoes of chemical precursors.

    See my previous comment. How does it work, this distinguishing of intelligence? Explain your method.

  295. 295
    ET says:

    Antonin on the key/ lock analogy:

    It’s a very misleading analogy for biological systems.

    Just saying it doesn’t make it so. You actually have to make a case, which you cannot.

    Chemical interaction is not all or nothing.

    That all depends, doesn’t it?

  296. 296
    ET says:

    Antonin:

    How does it work, this distinguishing of intelligence?

    What does that even mean? Everything we know says that codes only arise from intelligence.

  297. 297
    Antonin says:

    Everything he says about ID is flawed. Even a layperson can point out the obvious flaws in Felsenstein’s criticisms of ID.

    Are you that layperson? If it’s so easy, please demonstrate! 😉

  298. 298
    ET says:

    Antonin:

    KF, when you, Eric, gpuccio, anyone who thinks ID has some usefulness as an approach in understanding biological systems, can tell the difference between DNA sequences that have some biological activity from those that don’t, without synthesizing them, then I’ll revise my view on ID.

    Total gibberish. Science is made by making observations and trying to figure it out. We observe that certain DNA sequences code for proteins. Only a complete imbecile would say that ID needs to say what sequences code for something and which ones don’t.

  299. 299
    ET says:

    Antonin- I have already proven that Joe F doesn’t know anything about ID and his criticisms amount to nonsense and strawman erecting.

  300. 300
    Antonin says:

    What does that even mean?

    Have I misunderstood? Some DNA sequences result in the synthesisi of important proteins essential in the life of a cell. Gpuccio claims such sequences are rare. My question is how does he know. How can we know if an unknown sequence has biological activity or not without testing it in vitro.

    Does ID not purport to address this?

  301. 301
    Antonin says:

    I have already proven that Joe F doesn’t know anything about ID and his criticisms amount to nonsense and strawman erecting.

    Where’s the proof? Do you have a citation?

  302. 302
    kairosfocus says:

    Antonin, we have known about the genetic code and its role in protein synthesis for what 50+ years. That is what you have to face and come to terms with. Language used algorithmically in the heart of cell based life. And yes, as part of that we have key-lock fitting components. KF

  303. 303
    ET says:

    Antonin:

    Does ID not purport to address this?

    No.

    My question is how does he know.

    Biology 101- read the literature. No one thinks that every DNA sequence codes for proteins.

    Where’s the proof?

    In everything he writes about ID contrasted with what the ID experts say.

  304. 304
    Antonin says:

    Antonin, we have known about the genetic code and its role in protein synthesis for what 50+ years.

    Eugene Koons wrote a paper in 2009 reviewing the various theories proposed for the evolution of the genetic code. It’s worth a read.

    That is what you have to face and come to terms with. Language used algorithmically in the heart of cell based life. And yes, as part of that we have key-lock fitting components.

    Texas sharpshooting. Because things are how they are now, does not mean things were not different in the past.

  305. 305
    Antonin says:

    ET

    I doubt I’m alone in concluding exchanging comments with you is not productive. I see you made no attempt to support your ludicrous claim regarding “disproving” Felsenstein. Life’s too short to waste it engaging with blowhards.

  306. 306
    Bob O'H says:

    Es
    ric @ 272 – if ASC is a hypothesis test w.r.t. a specific hypothesis, then you should be able to provide the maths to show how you go from the hypothesis to ASC as a test statistic. I can see how you can do that for CSI (because of the relationship between Shannon’s entropy and the multinomial distribution), but not ASC.

    kf @ 274 – if you have a strong enough maths background, then you should be able to appreciate what I’m asking for, so you’ll also understand that you’re arm waving, and not providing the maths to back up your argument. If you don’t want to feel you’re being condescended to, then do the work to bring your arguments up to standard.

  307. 307
    Nonlin.org says:

    EugeneS @263

    Entropy is used both in thermodynamic systems and information theory (aka data transmission) courtesy of Claude E. Shannon.

    How is an observer surprised other than by observing data? Think telecommunications. The receiving observer is looking at nothing other than data. Same when you read memory devices.

    As explained, “Functional information” is a superfluous addition to ORDER. See @189, @248, etc.

  308. 308
    kairosfocus says:

    Antonin, it is increasingly clear that you are not engaging on substance. Have you read, say p. 5 of Crick’s letter to his son of March 19, 1953? Take time to ponder this: “Now we believe that the DNA is [–> underscore in Crick’s original] a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)” Your quarrel is with Crick et al and those who awarded relevant Nobel prizes, not me. In short, as the emphatic remark put it, the point was understood from the beginning. Further to this, note, the code is antecedent to cell based life, indeed it is constitutive of protein-making. Worse, we have a system of high complexity that all has to work together for it to “go.” A system, which pivots on language. Tossing out “Texas sharpshooter” or “evolution” as though they answer to the system and its requisites of function just does not cut it. This is not analogous to painting a target around where a bullet happened to hit, it is a natural target: you have to have a language in hand before you can use it to create a computer code and its associated execution machinery. That’s why Koonin speaks of an enigma in his title, disclaims having a definitive answer in his abstract then concludes it: “A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system.” KF

  309. 309
    kairosfocus says:

    BO’H: you were here all along and know the linked discussions in the literature which more than fulfill any real question you have. That’s why at this point I don’t take your attempt to dismiss seriously. Were I to take the time to reprise a lot of info theory and its mathematical foundations then belabour the obvious, that functionally specific complex organisation and associated information are real, it would make no difference to your rhetorical stance. How do I know this? because that is just what you have patently already done. So, I simply point out that the alphanumerical code in your own comments exemplifies FSCO/I and belies your arguments. That same phenomenon is found in the living cell, starting with protein synthesis. The ability to measure information is as commonplace as the size metrics on thumb drives or hard drives and file sizes. Functionality vs failure to function is readily observable. Metric models to identify information content of proteins, D/RNA etc are all on the ground. The sort of simple Fermi estimate I did above is sufficient to show why life forms contain FSCO/I well beyond what blind chance and/or mechanical necessity can plausibly explain. This means the best empirically warranted explanation is intelligently directed configuration. When you can show us an actually observed case of blind needle in haystack search creating FSCO/I, then you have a leg to stand on. As at now, we have trillions of cases of observed FSCO/I by design, nil by blind mechanisms. Rhetoric about hand waving will not change that fact. KF

  310. 310
    Nonlin.org says:

    EricMH @273

    ALL systems are a mix of ORDER and [what looks like, but is observational unknowable] RANDOMNESS. But some have very little order. For instance the position of a few isotopes within a bar of the same metal. Also, in radioactive decay, we cannot predict the order of decaying atoms.

    Distilling the whole universe to conclude “design” is not feasible. That’s why we need to focus on specific aspects of specific subsystems. I gave you a clear example @251.

    No, the fact that something exists rather than nothing is not necessarily order. Why would you conclude that?

  311. 311
    kairosfocus says:

    Nonlin,

    I think I need to cite Orgel:

    . . . In brief, living organisms are distinguished by their specified complexity [–> which is of course cashed out as bio-functionality from nanomachines in the cell to organ systems and body plans]. Crystals are usually taken as the prototypes of simple well-specified structures [–> order: break a crystal and the structure based on unit cells remains, just in two broken pieces], because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified [–> randomness, break this and it’s just two random lumps]. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity [–> observe two buckets are not enough, a third is required; break a cell in the right way and function breaks . . . ] . . . .

    These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure. [–> this is of course equivalent to the string of yes/no questions required to specify the relevant “wiring diagram” for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002.] One can see intuitively that many instructions are needed to specify a complex structure. [–> so if the q’s to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions. [–> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes. [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.

    See why?

    KF

  312. 312
    Nonlin.org says:

    KF,

    Design is not necessarily Life. We’re trying to detect Design.

    Necessity is Design to the best of our knowledge. So crystals too are designed (best inference). Are you saying they are not? if so, please prove.

    I know and understand very well the claim of “specified complexity” (yes, gpuccio and others did a good job explaining), but I am not sure you and others understand as well my claims.

    So, we can continue to monologue past each other, or we can zoom in on our differences and resolve them. So what will it be? 🙂

  313. 313
    gpuccio says:

    Antonin:

    “Of course he’s going to be able to more eloquently point out the flaws in your approach.”

    Then how can you be so sure that those flaws exist?

    “Maybe somebody who reads this site and also reads The Skeptical Zone could remind him of your latest comments.”

    Maybe. But my argument of the thief was explicitly addressed to him, and was a clear criticism of a statement he had made in a comment to me. On a thread about my arguments, if I remember well. At the time we were having some parallel discussion. It’s really unlikely that he has not read that point. And yet, to my best knowledge, he has not answered it.

    “And, I repeat, the lock/key analogy is misleading for the very reason you state.”

    Again, it’s not misleading at all. Its purpose was simply to clarify the concept of functional information. That it does very well.

    “There is no prize for a near miss.”

    There is no prize for a near miss in biology too. The target space, of course, is bigger, and is not 1. But if you miss it, even near-miss it, you get no prize.

    The prize is NS. Therefore, you have to get the function, so that it can be naturally selected for a definite reproductive advantage. Otherwise, there is no prize. So, if you miss the target space, there is no prize at all.

    “In biology, life’s diversity demonstrates there are many solutions to finding a living.”

    Of course there are many solutions. Most of them very complex. You are simply assuming that those solutions are not designed. This is, absolutely, assuming the consequent.

    “As I’ve said, I don’t think your approach is persuasive. I don’t think it is an accurate model of reality.”

    Ah, that is really an argument!

    You say my approach is not persuasive. Nonlin says that my arguments are unconvincing. Facing such strict counter-logic, I will certainly have to change my mind. 🙂

    “Chemical interaction is not all or nothing.”

    Of course. That’s why the target space in proteins is not one, but rather big. And yet, functional information can be extremely huge, because the search space is very very, very big.

    “KF, when you, Eric, gpuccio, anyone who thinks ID has some usefulness as an approach in understanding biological systems, can tell the difference between DNA sequences that have some biological activity from those that don’t, without synthesizing them, then I’ll revise my view on ID.”

    Then there is no hope that you revise them, because you simply don’t understand the issue.

    Of course the real final proof of how big is the target space would be to synthesize all possible sequences and test them for function. And the only final proof of the imagined existence of pathways that bring to complex functional proteins would be to sythesize all possible pathways and intermediates and test them for function and NS.

    But both you and I understand well that those procedures are not available in an exponential field. And never will.

    So, are we destined to never know?

    Luckily, that’s not true. Science has many indirect ways to draw reasonable conclusions in other ways.

    What a pity that darwinists have not been able to show any indirect evidence of the existence of those pathways.

    What a pity that sequence conservation, which is a pillar of neo-darwinian theory, clearly tells us a lot about the huge functional information in proteins.

    What a pity that you defend a false ideology without even being able to give any argument in its favour.

  314. 314
    Antonin says:

    KF:

    the code is antecedent to cell based life…

    This is far from certain. Koonin suggests several scenarios where evolution from simpler codes could have occured.

    …indeed it is constitutive of protein-making.

    And it is far from certain that proteins were required for the earliest forms of life. RNA has catalytic ability, even conserved in the ribosome today.

    Worse, we have a system of high complexity that all has to work together for it to “go.”

    Again, far from certain. More Texas sharpshooting! 🙂

    A system, which pivots on language.

    Not true. There’s no language involved in protein synthesis.

  315. 315
    Antonin says:

    gpuccio:

    It’s really unlikely that he has not read that point. And yet, to my best knowledge, he has not answered it.

    Well, let’s hope someone passes on a reminder. Professor Felsenstein only seems to comment at The Skeptical Zone occasionally and maybe he has other calls on his time.

  316. 316
    Antonin says:

    Gpuccio:

    Of course the real final proof of how big is the target space would be to synthesize all possible sequences and test them for function. And the only final proof of the imagined existence of pathways that bring to complex functional proteins would be to sythesize all possible pathways and intermediates and test them for function and NS.

    A start has been made with sampling. Is it a reasonable assumption that functionality is evenly distributed? Is it a reasonable assumption that functionality such as binding affinity can vary from zero through to a local maximum? Is it a reasonable assumption that the same function can be carried out by different sequences?. (And of course, living organisms have been coming up with novel functions since the dawn of life)

    But both you and I understand well that those procedures are not available in an exponential field. And never will.

    Did you mean “experimental”? I think progress is being made. I have high hopes that, one day, computer modelling of unknown proteins will become good enough to predict functionality.

  317. 317
    jawa says:

    Favor request:

    Can the same person asking Professor Felsenstein to answer gpuccio’s comments addressed to him long ago, also let University of Kentucky professor Arthur Hunt know that many curious readers are still waiting for his reply to gpuccio’s comments addressed to him? Thanks.

    Does anybody else wonder why these professors ran away when the discussions got deep into real evidence territory?

    Any thoughts?

  318. 318
    kairosfocus says:

    NL, cell based life is a relevant example. KF

  319. 319
    kairosfocus says:

    Antonin, there is only one actually observed biological life that is metabolic and self-replicating. It is based on the living cell and uses proteins coded for in DNA using one or other dialects of the well known genetic code. First provide an observation of a different system architecture then equally empirically grounded bridging steps. Absent that we see empty, ideology-serving speculation. Speculation unwarranted by Koonin, who — again — starts his paper with the term “enigma” and ends his abstract with a telling confession: “A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system.” KF

  320. 320
    Antonin says:

    Can the same person asking Professor Felsenstein to answer gpuccio’s comments addressed to him long ago, also let University of Kentucky professor Arthur Hunt know that many curious readers are still waiting for his reply to gpuccio’s comments addressed to him? Thanks.

    I’ve not seen Professor Hunt commenting at The Skeptical Zone. I have seen him commenting at Peaceful Science, Josh Swamidass’s site. Art’s email address is published on his website, so why not just email him?

    Does anybody else wonder why these professors ran away when the discussions got deep into real evidence territory?

    There’s an assumption in your question. If fact there are two. I think it might have been attributed to Richard Dawkins; a remark along the lines of “it might look good on his CV but it won’t look good on mine.” Some interactions prove not to be worth the effort. See ET above. 🙂

  321. 321
    Antonin says:

    KF:

    Antonin, there is only one actually observed biological life that is metabolic and self-replicating.

    Of course! Glad to see we agree on universal common descent.

  322. 322
    jawa says:

    Antonin @319:

    we all know why those distinguished professors ran away from the heat of a serious discussion with gpuccio, it’s obvious: lack of solid arguments.

    nothing to do with CV or anything like that

    quite on the contrary, proving an ID proponent like gpuccio wrong would have definitely made their CVs shine with bright colors.

    what doesn’t look good in their CVs is to publicly lack arguments in a serious discussion with an ID proponent.

    in such a case, it may look better to find cheap excuses to be conspicuously absent from the discussion.

    that’s all. very simple.

  323. 323
    jawa says:

    structural function or functional structure?

    is a structure determined by a given function (i.e. created for that function) or a function determined by a given structure?   

    is a helicopter created to fly or flying is an emerging property of a helicopter?

    is a ship created to navigate or navigation is a function derived from the ship structure?

    is a truck made to transport cargo or that is just an emerging property of trucks?

  324. 324
    daveS says:

    quite on the contrary, proving an ID proponent like gpuccio wrong would have definitely made their CVs shine with bright colors.

    Somehow I can’t imagine Joe Felsenstein boasting about his exchanges with blog posters on his CV…

  325. 325
    gpuccio says:

    daveS:

    Probably not, I agree. 🙂

  326. 326
    Mung says:

    Antonin:

    Koonin suggests several scenarios where evolution from simpler codes could have occured.

    A simpler code is still a code.

  327. 327
    gpuccio says:

    Antonin at #315:

    “Is it a reasonable assumption that functionality is evenly distributed?”

    I don’t understand what you mean. Could you explain better? “Functionality”, in particular, seems to mean nothing specific. As I have said many times, but you seem to willingly ignore, anything can be functional: stones, mountains, watches, proteins. It all depends on the functions you define, and on their complexity.

    “Is it a reasonable assumption that functionality such as binding affinity can vary from zero through to a local maximum?”

    And so? You should look for something that can be naturally selected, giving a definite reproductive advantage. “Binding affinity” will not do.

    “Is it a reasonable assumption that the same function can be carried out by different sequences?”

    This is obviously true. But it’s not an assumption, We have good evidence of that. And so?

    “And of course, living organisms have been coming up with novel functions since the dawn of life”

    Of course, and so? Are you again assuming the consequent, that they were not designed?

    “Did you mean “experimental””

    No. I meant exponential. IOWs, as the number of possible sequences incresases exponentially, testing all possible sequences for anything is empirically impossible even for short proteins. That’s what I meant.

    “I have high hopes that, one day, computer modelling of unknown proteins will become good enough to predict functionality.”

    I have good hopes for that too. And then we will know. That’s what I mean by an “indirect method”.

    But we are still far from that. So, in the meantime, we should sticj to other indirect methods, and try to understand.

    In the end, I can’t see any argument coming from you. OK, that’s fine just the same. Thank you for trying, anyway.

    Just a hint. As the best example of a new function arising from a completely random series of mutations is chloroquine resistance, that starts with two independent and individually non functional mutations, you could maybe try to explain how the alpha and beta chians of ATP synthase originated form a two AAs functional sequence, by gradual NS of intermediates.

    OK, let’s say that you can start with a 5 AAs functional sequence. I feel generous today.

    Do you really believe that a 5 specific AAs sequence can be useful in the context of the F1 subunit of ATP synthase and be therefore naturally selected?

    And that we can add one AA at a time, gradually increasing its functionality so that each time the new result can be naturally selected, and cancel the previous stage?

    Up to the current (and extremely ancient) form of the two chains, for a total number of 1082 AAs, 625 of which are conserved between E. coli and humans?

    Just to know how much your imagination can be fueled by dogma.

  328. 328
    Mung says:

    kairosfocus:

    I think I need to cite Orgel

    Probably can’t do that enough times. 🙂

    It’s not like IDists invented the idea of applying information to biology.

  329. 329
    gpuccio says:

    Antonin:

    Koonin writes:

    The structure of the SGC—that is, the mapping of 64 codons to 20 amino acids and the stop signal—is manifestly regular with respect to multiple criteria (44, 84). This nonrandomness of the code seems to require an explanation.The threemost advanced and coherent concepts that strive to explain regularities in the code are the stereochemical, coevolution, and error minimization theories (18, 39, 44). We apply the term theory hereinafter for the sake of brevity and following the tradition, although none of the scenarios of code evolution seems to meet the criteria of a theory in the strict sense. Arguably, the frozen accident perspective also has to be taken into account in conjunction with any of the above concepts.

    Emphasis mine.

  330. 330
    OLV says:

    Off topic:
    Seeing is believing: the Bicoid protein reveals its path
    SDD:  synthesis-diffusion-degradation

    the SDD model was irrefutable for more than two decades until first doubts were raised in 2007 regarding the diffusion properties of Bcd associated with the SDD model. This led to re-thinking of the issue and the definition of a new model, termed the ARTS model which could explain most of the physical constraints that were inherently associated with the SDD model. In the ARTS model, gradient formation is mediated by the mRNA which is redistributed along cortical microtubules to form a mRNA gradient which is translated to form the protein gradient. Contrary to the SDD model, there is no Bcd diffusion from the tip. The ARTS model is also compatible with the observed cortical movement of Bcd.

    Another one bites the dust!

     
    Now, the ARTS model raises new questions.

    Time to rewrite textbooks, again?

  331. 331
    OLV says:

    a paper apparently associating structure with function?

    Dorsal root ganglion (DRG) neurons are the first neurons of the sensory pathway. They are activated by a variety of sensory stimuli that are then transmitted to the central nervous system. An important feature of DRG neurons is their unique morphology where a single process -the stem axon- bifurcates into a peripheral and a central axonal branch, with different functions and cellular properties. Distinctive structural aspects of the two DRG neuron branches may have important implications for their function in health and disease. However, the link between DRG axonal branch structure, polarity and function has been largely neglected in the field, and relevant information is rather scattered across the literature. In particular, ultrastructural differences between the two axonal branches are likely to account for the higher transport and regenerative ability of the peripheral DRG neuron axon when compared to the central one. Nevertheless, the cell intrinsic factors contributing to this central-peripheral asymmetry are still unknown.

  332. 332
  333. 333
    Mung says:

    Antonin:

    Chemical interaction is not all or nothing. ATP affinity, for example, is a variable depending on binding energy. A safe key either opens the safe or doesn’t.

    Yes, a key either opens the lock or it doesn’t. So what. Two molecules bind or they don’t. The same key can can more than one lock. Is that a concept that is unfamiliar to you?

  334. 334
    Mung says:

    EugeneS:

    Entropy is a function of state of a thermodynamic system provided the given system can be described as a thermodynamic one, which is not always the case.

    Yes.

    E.g. our universe as a whole is not a thermodynamic system.

    And the phrase “the entropy of the universe” is nonsense. 🙂

  335. 335
    Mung says:

    DaveS @ 218:

    I have no idea how to do that step.

    It was a trick question. 🙂

  336. 336
  337. 337
    jawa says:

    gpuccio @326:

    “OK, let’s say that you can start with a 5 AAs functional sequence. I feel generous today.”

    Generous seems like an understatement. 🙂

  338. 338
    jawa says:

    gpuccio @326:

    “Just to know how much your imagination can be fueled by dogma.”

    Their imagination seems unlimited.

  339. 339
    kairosfocus says:

    Antonin, there we go off on another tangent. FYI, common design will work just as well and is not the contradiction of particular or universal common descent. That is, CD is strictly irrelevant to the question. What is key here is that there is essentially one kind (note the genus in the logical sense) of metabolising, self-replicating biological life, cell based; despite biodiversity that proverbially ranges from amoeba to man (note the differentia). Even macro-scale life forms that do not use separate cells are clearly derivative. What is focal, is that a central process in such life uses code-based protein synthesis. That code is string based and alphanumerical. This points to a cybernetic system that is essentially linguistic, codes being an application of language. Language is an extremely complex phenomenon, so we are dealing with a lot more than the direct info content of the code-bearing D/RNA strands or even the organised molecular nanotech. And even just that is already well beyond a plausibility threshold for blind chance and/or mechanical necessity. The only empirically warranted cause of such phenomena is intelligently directed configuration, with trillions of cases in point. KF

  340. 340
    kairosfocus says:

    PavelU, kindly observe that the argument presented is within the system, i.e. it is discussing tRNA’s. tRNA molecules fold and function by working with ribosomes and dozens of other components to synthesise proteins. A key point is, that they are in effect position-arm molecular taxi-cabs with in-common CCA tool-tip ends. That is the coding is expressed by loading the correct AA based on recognition of the conformation of a given tRNA (of the twenty in question) by a loading enzyme; chemically, the tips are the same and are in effect a universal socket. Enzymes of course are within the system, closing the loop. As this is central to protein synthesis, claimed strong arguments as to blind watchmaker evolutionary origin will have to account for the system as a whole not simply point to a pattern of elements within the system, and they have to account for relevant empirical observations so that it is not just a reading with the eye of evolutionary materialistic faith. KF

  341. 341
    jawa says:

    KF,
    Agree with you.
    The argument presented in the paper cited by PavelU @335 has no strength whatsoever. If one disects it deeply then new questions are raised. That’s flaky at best. He should try again.

  342. 342
    Antonin says:

    mung:

    Yes, a key either opens the lock or it doesn’t. So what.

    An ideeal lock is opened by a key with the correct pattern. Say there are a 1,000 possible variations in key pattern. Matching lock to key is siply the laborious task of trying each one in turn. No clue is offered when trying a key that is close to the unique combination. Chemical affinity between molecules is a variable. Molecules can repel each other, or be attracted in varying intensity. Given a situation where a production system of molecules is a little promiscuous, selection will concentrate those molecules with higher affinity.

    Two molecules bind or they don’t.

    See the difference?

    The same key can can more than one lock. Is that a concept that is unfamiliar to you?

    I can see that sensible discussion with you is unlikely. I’ve been following Peaceful Science and The Skeptical zone recently. Your reputation precedes you. Unless there is more than one mung, in which case, I’ll reserve judgment.

  343. 343
    Antonin says:

    KF:

    common design will work just as well

    Until you or anyone propose a mechanism, this is wishful thinking.

  344. 344
    Antonin says:

    Antonin at #315:

    “Is it a reasonable assumption that functionality is evenly distributed?”

    I don’t understand what you mean.

    Any combination of amino acids can be theoretically strung into a sequence. The number of such molecules is 400 for a dipeptide and rises exponentially with each additional aa. The formula is N to the power 20 (assuming a pool of 20 aas). We could reasonably assume some are biologically active in some context. What we don’t know is how sparse that activity is among the general population of theoretical proteins nor do we know whether activity is spread evenly. You seem to be assuming, not just sparseness, but uniqueness with no possibility of modification producing increased biological activity.

  345. 345
    Antonin says:

    Just occurs to me. Mung posts regularly at The Skeptical Zone. Can he pass on gpuccio’s request that Joe Felsenstein take a look at gpuccio’s “thief” scenario?

  346. 346
    Antonin says:

    gpuccio:

    Do you really believe that a 5 specific AAs sequence can be useful in the context of the F1 subunit of ATP synthase and be therefore naturally selected?

    And that we can add one AA at a time, gradually increasing its functionality so that each time the new result can be naturally selected, and cancel the previous stage?

    At last, some meat in the sandwich! 🙂

    These are good questions and I will try and give my best answer. Stay tuned.

    ETA: It won’t be the answer to life, the universe and everything. That has been answered already!

    42

  347. 347
    Antonin says:

    Oh and thanks to PavelU for the link.

  348. 348
    Antonin says:

    Oops!

    Correction: “The formula is N to the power 20 (assuming a pool of 20 aas).” Should read:

    The formula is 20 to the power N!

  349. 349
    jawa says:

    Here’s an example of designed adaptation:

    While the 737 Max 8 is billed as a new jetliner, it is closely adapted from earlier versions of the Boeing 737.
    Washington Post article

    In this case, since the conscious designer is human, design errors are possible. However, even if the design is correct, errors could have been made during the development and testing of the object. Also, the given object could have been designed to operate under certain conditions and to be maintained according to some strict specifications that must be carefully met.

    Some analogies could apply to the biological area.

  350. 350
    jawa says:

    There are gazillion examples of common design all around us in this world.
    Wake up and smell the flowers!

  351. 351
    Antonin says:

    So, in the meantime, we should sticj to other indirect methods, and try to understand.

    In the end, I can’t see any argument coming from you. OK, that’s fine just the same. Thank you for trying, anyway.

    I decided to comment here precisely to communicate with gpuccio. I think gpuccio has not got an accurate model with which to assess the evolvability of biological systems. Gpuccio seems to have understood the two basic points I am making: firstly about the inappropriateness of his model and secondly about taking it to a wider world for more effective feedback and criticism. That was the height of my ambition

    Just a hint. As the best example of a new function arising from a completely random series of mutations is chloroquine resistance, that starts with two independent and individually non functional mutations, you could maybe try to explain how the alpha and beta chians of ATP synthase originated form a two AAs functional sequence, by gradual NS of intermediates.

    I’m Catholic. I believe in the Creation. I also think God created us with the curiosity and skills to better understand His creation. The Old Testament is a set of stories appropriate for the comprehension of the people who lived at that time. I could just say God decided to do it that way but God allows us to discover for ourselves. We can observe, we can hypothesize, we can experiment. One thing that doesn’t help our understanding is to persist with inaccurate models of reality.

    One thing Creationists overlook is method. God did it but do not ask how did He do it? For this we can use the scientific method. Regarding biology, the aim is ambitious. Explain the origin of life (the method God used to create life) and explain life’s subsequent diversity. This entails in total explaining all the steps from living organisms first existing and every subsequent step to arrive at the unbroken chain of descent between every single living organism today and all it’s predecessors. Yet we have a mechanism that can explain many of these events. A process whereby organisms are shaped over time by their environment (part of God’s creation) and by changes and feedback in that environment. We know the heritable element, we know how that can vary and we know how genetic change can be selected for by the environment surrounding the organism.

    OK, let’s say that you can start with a 5 AAs functional sequence.< I feel generous today.

    But not ambitious. 🙂

    Do you really believe that a 5 specific AAs sequence can be useful in the context of the F1 subunit of ATP synthase and be therefore naturally selected?

    And that we can add one AA at a time, gradually increasing its functionality so that each time the new result can be naturally selected, and cancel the previous stage?

    No, I don’t. As I keep saying, your model is inaccurate. Taking one instance of an existing protein, I think that mutation, duplication, recombination and so on can introduce variation that can be selected for or against and adopted or eliminated. With reiteration, this is a powerful agent of change.

    Up to the current (and extremely ancient) form of the two chains, for a total number of 1082 AAs, 625 of which are conserved between E. coli and humans?

    But I do think that selection conserves proteins with the best function. And so why shouldn’t proteins that do the best job be retained both by modern E. coli and humans. Commonality runs much deeper than that.

    Just to know how much your imagination can be fueled by dogma.

    Oh, I realise the depth and breadth of the problem that biologists have in explaining everything biological. But the same explanation fits the facts. And ID does not have an alternative explanation. At. All.

  352. 352
    kairosfocus says:

    Antonin, it is a commonplace that design is effected by intelligently directed configuration. If you mean, a technology, we already see first steps in that direction through Venter et al (working in molecular nanotech labs), and all reasonably informed people are aware of genetic modification, indeed there is a panic on genetic engineering of foods. There is concern over genetic manipulation of microbes to create novel weapons of mass destruction; such, you cannot be reasonably ignorant of. The proposed mechanism that lacks empirical warrant is origin of codes, algorithms, effecting molecular nanomachinery etc by blind chance and/or mechanical necessity in Darwin’s pond or the like environment. Then, origin of novel body plans from amoeba to us runs into at least as stiff an origin of information challenge. And if you mean to reduce the mind to blind mechanisms on an equally blindly arrived at computational substrate (likely through the question begging ideological imposition of evolutionary materialistic scientism and/or fellow traveller notions) then that is self-defeating by way of undermining responsible, rational freedom. Likely, your problem is worldview and ideology dominating the needed inductive reasoning and empirical foundations of science, not science. KF

  353. 353
    kairosfocus says:

    Antonin, attempted personal dismissiveness only reveals that you will not acknowledge that master keys exist such that one key may open many diverse locks. By, of course, common design. Where, BTW, we already have a major clue of common design in the common code (notwithstanding dialects and oddball mods) used to create proteins. Please, refocus on the issue. KF

  354. 354
    Antonin says:

    Antonin, attempted personal dismissiveness

    I’ve definitely dismissed ET, provisionally dismissed mung. I’m still talking to you, notwithstanding your pompous asides.

    …only reveals that you will not acknowledge that master keys exist such that one key may open many diverse locks.

    Does your obtuseness know no bounds? 🙂 Of course master keys exist. They are irrelevant as an analogy in biology. At the molecular level, all molecules with the same stereochemistry in the same substrate are identical. No way to tell one water molecule from another. But chemical affinity between molecules will vary depending on their precise chemical structure and configuration. All identical molecules are identical and water is wet.

    By, of course, common design. Where, BTW, we already have a major clue of common design in the common code (notwithstanding dialects and oddball mods) used to create proteins. Please, refocus on the issue.

    I’m not disputing God created the Universe and everything in it. I’m pointing out that He hasn’t hidden anything and we have at least some ability to look and learn. Your talk of language in the context of chemistry leads you to a dead-end in understanding.

  355. 355
    gpuccio says:

    Antonin:

    A few clarifications:

    We could reasonably assume some are biologically active in some context.

    “Biologically active in some context” is really vague. Too easy! The correct requirement is:

    “We could reasonably assume that some are naturally selectable”.

    It’s all another thing. Why don’t you say things as they are, at least according to the model you are defending?

    What we don’t know is how sparse that activity is among the general population of theoretical proteins nor do we know whether activity is spread evenly.

    I can agree that we don’t know exactly, but we can certainly understand a few important things from known facts.

    For example, the mere existence of about 2000 protein superfamilies that are completely separate at the three levels of sequence, structure and function certainly tells us that many important biological functions are isolated islands in the sequence space. As I have always argued.

    You seem to be assuming, not just sparseness, but uniqueness with no possibility of modification producing increased biological activity.

    Completely false. I can’t understand why you keep misrepresenting my thoughts. Do you even read what I write?

    a) I do believe in sparseness (I don’t “assume” it, I infer it from known facts, as I have tried to explain in the previous point).

    b) But certainly I don’t assume uniqueness:

    From my comment #312 (to you):

    “Of course. That’s why the target space in proteins is not one, but rather big. And yet, functional information can be extremely huge, because the search space is very very, very big.”

    What is not clear in that statement?

    c) I am not assuming that there is “no possibility of modification producing increased biological activity”. Indeed, I have always claimed the opposite:

    See here:

    What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/

    Just as an example of an argument I have made many times, I paste here my comment #320 in that thread:

    To all interested:

    So, let’s see which are the specific features present in practically all the best knwon examples of generation of some functional information by the RV + NS algorithm, practically the only real evidence for neo-darwinism as an explanatory theory:

    1) The starting point of the process is always an already existing, complex and functional structure.

    2) The first step is always effected by RV only: it is alwatys a small variation of the pre-existing structure. That variation is usually of one single mutation (4 bits at most), but we have good examples of two mutations, (8 bits most), like in chloroquine resistance. I am not aware of initial random steps of 3 mutations, but they could in principle exist. I doubt that 4 random mutations steps are feasible.

    However, the point is not so much where exactly the edge is. The point is that the probability of a first random step decreases exponentially with each new mutation necessary to reach the basic selectable function. We know that in chloroquine resitance the frequency of the two mutations event is dramatically lower than the frequency of a single mutation event in other antibiotic resistance scenarios. The paper “waiting for two mutations” gives us a good idea of how difficult a two mutations event is in reality.

    So, let’s calll this concept the edge of random evolution. I believe that Behe is correct in proposing two mutations: that is probably the real edge in the general case. But I can grant 3 mutations, in exceptional cases, and even 4 mutations as an extreme value, just to be generous.

    So, let’s say that the edge of random evolution is 2 – 4 mutations (at most, 8 – 16 bits).

    That basic starting function can now be naturally selected and fixed, with a probability which depends on many factors (I will be back on that).

    3) If there is a continuous functional space around the original basic starting function, a few new mutations can accumulate, optimizing the original function.

    What is a continuous functional space?

    It’s simple. In this case, it just means that there are, among all the possible one aminoacid substitutions, one or more that improve the original basic function.

    In the case of CR, we have seen that such a thing is true. Indeed, there is more than one possible selectable pathway.

    It is important now that each successive step be simple (one mutation only), to avoid that new huge improbabilities accumulate for the process. Indeed, in the case of CR, all the successive selectable steps are of 1 mutation.

    Each successive step must be naturally selectable, IOWs it must improve the original function. So, a ladder of naturally selectable and simple (1 mutation) steps can be available to reach the final target.

    So, how many mutations can be added by NS?

    In the case of CR, we have observed only pathways that add 2 or 3 mutations to the original 2, for a total of 4 or 5.

    In the case of penicillin resistance in pneumococcus, I quote from the recent paper I already referenced:

    “The individual reversion of the 41 substitutions of a transpeptidase domain of PBP2x from a particularly resistant strain uncovered the role of four mutations, I371T, R384G, M400T and N605T, in addition to those in positions 338 and 339 (Carapito et al., 2006) (Fig. 8). Reversion of the six substitutions nearly restored a normal and rapid acylation rate. Introduction of five of the substitutions into PBP2x from a susceptible strain diminished the reactivity with ?-lactams, almost to the level of the original PBP2x from the resistant strain. These effects measured in vitro were mirrored by the expected phenotypic consequences in vivo (Carapito et al., 2006). With a different PBP2x, a similar experiment where the effect of individual reversions was directly monitored in vivo also identified positions 371 and 384 as important (Smith & Klugman, 2005).”

    Here, too, the number of useful total mutations that can optimize the resistance is in the same range: 2 – 6.

    So, we can define that as the edge of simple optimization : in well known cases, let’s say it is 6 total mutations, IOWs adding, with the help of NS, 4-5 single mutations to the original 1-2 mutations random event.

    6 total mutations is a functional information of, at most, 24 bits.

    A very simple concept should be clear: in all these well known cases, the intervention of NS acts only to otpimize the existing new function which was created in the first step as a slight random modification of the original functional structure: in the case of antibiotic resistance, the modification of an existing function which indirectly confers some resistance ot the antibiotic.

    That brings us to the next point:

    4) All these well known cases can be defined as cases of loss of function mutations which indirectly confer an advantage in a specific selective environment.

    Let’s call this kind of mutations: beneficial loss-of-function mutations.

    The term is not mine. I quote from this recent and interesting paper:

    “The spectrum of adaptive mutations in experimental evolution”

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268012/

    The availability of beneficial loss-of-function mutations and the large target size for these events ensures that these mutations will come to dominate experimental evolution over short time scales.

    Emphasis mine.

    The point is very simple: loss of function mutations are very simple, even those which are in a sense “beneficial”. That’s why their “target size” is large. That’s why they are in the range of RV.

    We have seen that RV can give us, in most cases, only 1 or 2 mutations complexity. We have conceded 4, for the sake of discussion.

    That is enough to generate a loss of function in an existing structure, and in some cases an indirect beneficial effect through that loss of function.

    But it is definitely not enough to generate a new function from scratch!

    Not enough at all!

    And believe me, it’s not a question of the “short time scale”. Those guys have their math wrong.

    The important point is:

    Time scales improve the probabilistic resources linearly

    while:

    Adding new necessary mutations to the first step basic function increases the probabilistic barriers exponentially!

    There is no hope at all for RV, in whatever time scales, if we have to reach thresholds of, say, 35 AAs (140 bits). But even 10 AAs (40 bits) would be inconceivable.

    Remember, Szostak found a 40 bit function in a rather vast random library: weak ATP binding. But that was not a naturally selectable function, not at all. Only artificial selection, set up by intelligent researchers, could detect and select that kind of function.

    Who has ever found a 40 bit naturally selectable function in a random library?

    So, our important conclusion here is that:

    Only very simple functions can be the first step of a pathway, because the first step of a pathway can rely only on RV, and the power of RV in terms of generating functional information is really minimal.

    That’s why the only real examples that we can find are of the type “beneficial loss-of-function mutations”, because that kind of basic functions are the simplest type.

    Then you say:

    At last, some meat in the sandwich! ????

    These are good questions and I will try and give my best answer. Stay tuned.

    That’s good. I see you have already given your best answers, so I will comment on them in next post. 🙂

  356. 356
    kairosfocus says:

    Antonin,

    you begin to see that AA sequence space for the 20 dominant proteins runs as 20^N. That’s a beginning. Actually, with L and D forms (and a prebiotic envt would all but certainly be racemic) we look at 39^N.

    Blend in the other AA’s not used on the whole and we are looking at well over 100^N, taking in L and D forms.

    Then, we have to integrate the D/RNA’s, with similar challenges.

    Then, observe that such molecules are thermodynamically uphill, and deterioration dominates in any realistic prebiotic environment not intelligently manipulated to bring Le Chetalier’s principle to bear in intended ways.

    Now, ponder the von Neumann kinematic self replicator model for self replication, integrating needed metabolic nanomachines. Mix in encapsulation and smart gating. Bring on the codes and algorithms, requiring hundreds of correct form proteins, D/RNA’s, correctly organised and coupled. BTW, correct form proteins must be chained correctly so they can fold, agglomerate, add metal ions etc and fit together in key-lock fashion, where already we know of thousands of fold domains, many involving one or a few AA chains, scattered in no convenient tree-like pattern or continent of closely placed forms in AA sequence space.

    Contrast how many more ways the same atoms could be clumped at random or scattered.

    You will soon enough see why the metaphorical summary of islands of function in vast configuration spaces (= cut down phase spaces where only configuration is relevant) is relevant. Indeed, you can get the picture by putting a pile of ABU 6500 C3 reel parts in a bucket then shaking repeatedly, which will show how isolated functional configs are in the space of possibilities.

    In short, the island of function in an overwhelmingly large sea of non-functional configs challenge starts with OoL.

    It continues through origin of body plans all the way from amoeba to us.

    Where with 10^57 atoms in our sol system (98% in the sun) or 10^80 in the observed cosmos, 10^17 or so s available from the singularity, atomic rxn rates of 10^12 – 15 times per s, etc, we see that a config space that exceeds 500 – 1000 bits of complexity cannot reasonably be searched. Indeed, the fraction searched to the config space rounds down to negligibly different from zero.

    So, focus on the language, algorithms, code and coordination of execution machinery required. Complex, highly integrated, sophisticated, information-rich technology has just one empirically warranted cause.

    Design.

    KF

  357. 357
    Antonin says:

    KF:

    Antonin, it is a commonplace that design is effected by intelligently directed configuration. If you mean, a technology, we already see first steps in that direction through Venter et al (working in molecular nanotech labs), and all reasonably informed people are aware of genetic modification, indeed there is a panic on genetic engineering of foods. There is concern over genetic manipulation of microbes to create novel weapons of mass destruction; such, you cannot be reasonably ignorant of.

    This is irrelevant to biology. Inappropriate analogies between what humans are capable of has nothing to do with how life started and diversified.

    The proposed mechanism that lacks empirical warrant is origin of codes, algorithms, effecting molecular nanomachinery etc by blind chance and/or mechanical necessity in Darwin’s pond or the like environment. Then, origin of novel body plans from amoeba to us runs into at least as stiff an origin of information challenge.

    Argument by soundbite? There are milestones in the history of biological organisms from origin to now, sure. OOL itself, prokaryotes to eukaryotes, haploidy to diploidy, multicellularity, evolution of sex and meiosis, regulator genes. All deserve study.

    And if you mean to reduce the mind to blind mechanisms on an equally blindly arrived at computational substrate (likely through the question begging ideological imposition of evolutionary materialistic scientism and/or fellow traveller notions) then that is self-defeating by way of undermining responsible, rational freedom.

    Well, no problem there as I have no such ambition. I must say you have a very active imagination! (fellow traveller, indeed! LOL)

    Likely, your problem is worldview and ideology dominating the needed inductive reasoning and empirical foundations of science, not science.

    More likely, I have a different opinion from you of what science is and what science is not.

  358. 358
    Antonin says:

    …a pile of ABU 6500 C3 reel parts in a bucket…

    Good grief!

  359. 359
    kairosfocus says:

    PS: I see GP has commented on similar lines, from the protein superfamily angle. There can be endless archipelagoes of function, the problem is there are nowhere near enough resources to search on a sol system or observed cosmos gamut with any reasonable plausibility of success. And to resort to an unobserved quasi-infinite multiverse or the like is to move to philosophy. If you do that, the discussion moves to comparative difficulties across worldviews, ideologies and fellow traveller movements, and it is immediately clear that evolutionary materialistic scientism and fellow travellers is self-referentially self-defeating. (Start, with grounding duty to truth and right, responsible, fair-minded reasoning and the linked IS-OUGHT gap.)

  360. 360
    Antonin says:

    Just a question, KF. Who rolls DNA strands up into double helices?

    (Anyone can answer!)

  361. 361
    Antonin says:

    …the problem is there are nowhere near enough resources to search on a sol system or observed cosmos gamut with any reasonable plausibility of success…

    It would be a problem if the evolutionary process worked like that. Fortunately, for life on Earth, it doesn’t. There are no unique solutions. Searches don’t need to be exhaustive, Stumble across something better then you had before and you gain an edge on your competitors.

  362. 362
    kairosfocus says:

    Antonin, your two responses above are diagnostic. I could speak in abstract terms of node-arc meshes that must fit functional criteria, but the ABU reel makes the point directly. Where, BTW, the integration of a von Neumann self replication facility in the relevant case ADDS vastly to the complexity of the entity in question. Where BTW, if you read ch 2 of Paley’s Nat Theol, you will see he contemplated implications of such a self-replicating facility 150 years before JvN. Likewise, by pointing to Venter et al and molecular nanotech labs as well as to actual technologies, I demonstrated on empirically relevant basis that intelligently directed configuration is highly relevant, dismissive rhetoric on your part notwithstanding. I have already corrected your abuse of analogy. I remind you that material resemblance per genus-differentia may be highly cogent and instructive. In particular, apart from fallacious dismissive use of “analogy” you have given us no reason to disagree with Crick et al in recognising that D/RNA etc manifest alphanumeric 4-state digital code and linked deeply information-rich algorithms in action. And so forth, gotta go now. KF

  363. 363
    kairosfocus says:

    Antonin, where does the homochiral sequencing of DNA strands come from, so that key-lock fitting and van der Waals forces with available correctly chiral monomers allows for complementary, key-lock fitting storage of the information-rich sequence? Why is it that information-storage in such a string structure requires high contingency of successive monomers (bases, here) in the chaining, and what would be the implication of forced sequence along the chain (as opposed to complementarity at right angles to it allowing redundancy)? KF

  364. 364
    kairosfocus says:

    Antonin, start from a Darwin pond, comet core, gas giant moon, volcano vent or the like with reasonable chemistry then proceed by empirically warranted and thermodynamically plausible stages to a functioning encapsulated metabolic entity that self replicates using codes. When you can do so, you have something. Until then, you face the first level search challenge of vastly inadequate resources as described. Remember, we deal with highly contingent, configuration-dependent, information-rich entities. Rhetorically sweeping away the search challenge posed by OoL does not work as good scientific thinking. If you hope for search for a golden search, a search is a collection of subsets so searches for golden searches blindly search the power set of the original config space. If that has cardinality n, the power set has cardinality 2^n. If you imply laws of mechanical necessity have cell based life written into them as emerging by necessity or near necessity, that needs to be shown and would pose a fine tuning challenge tantamount to cosmological front loading on steroids. KF

  365. 365
    gpuccio says:

    Antonin at #350:

    I decided to comment here precisely to communicate with gpuccio.

    Here I am! 🙂

    I think gpuccio has not got an accurate model with which to assess the evolvability of biological systems.

    Let’s see why.

    Gpuccio seems to have understood the two basic points I am making:

    Let’s see.

    firstly about the inappropriateness of his model

    I have not “understood”. I have considered the few things you have said, and asnwered it showing that they were not correct.

    secondly about taking it to a wider world for more effective feedback and criticism.

    That is not a scientific argument. As explained, your “point” is about a personal choice that I am not available to discuss.

    That was the height of my ambition

    You seem very interested in ambition. Limiting yours, but ecouraging mine!

    I’m Catholic. I believe in the Creation. I also think God created us with the curiosity and skills to better understand His creation. The Old Testament is a set of stories appropriate for the comprehension of the people who lived at that time. I could just say God decided to do it that way but God allows us to discover for ourselves.

    I don’t discuss relious arguments here.

    We can observe, we can hypothesize, we can experiment.

    Of course.

    One thing that doesn’t help our understanding is to persist with inaccurate models of reality.

    That’s exactly my point about neo-darwinism!

    One thing Creationists overlook is method. God did it but do not ask how did He do it?

    I am not a Creationist. And, as said, I don’t discuss religious arguments here.

    For this we can use the scientific method.

    That’s what I try to do in all my arguments.

    Regarding biology, the aim is ambitious.

    Of course. (Ambition again?)

    Explain the origin of life

    A very important task.

    (the method God used to create life)

    That’s not the same thing.

    and explain life’s subsequent diversity.

    A very important task.

    This entails in total explaining all the steps from living organisms first existing and every subsequent step to arrive at the unbroken chain of descent between every single living organism today and all it’s predecessors.

    That’s certainly true.

    Yet we have a mechanism that can explain many of these events.

    Of course. It’s design.

    A process whereby organisms are shaped over time by their environment

    Oh, no! That’s not true. The environment has no idea of how the F1 subunit of ATP synthase can work. And yet, ATP synthase is essential to the development of life. Just to give an example.

    (part of God’s creation)

    Religion again? Are you a Creationist?

    and by changes and feedback in that environment.

    Simply not true. Change and feedbacks know nothing of how the F1 subunit of ATP synthase can work, Just to give an example.

    We know the heritable element, we know how that can vary and we know how genetic change can be selected for by the environment surrounding the organism.

    Very true. And what we know does not explain anything about ATP synthase, or complex functional information in general.

    But not ambitious.

    ! 🙂

    As I keep saying, your model is inaccurate.

    Let’s see why.

    Taking one instance of an existing protein

    For example?

    I think that mutation, duplication, recombination and so on can introduce variation that can be selected for or against and adopted or eliminated.

    And I agree about that. And so?

    With reiteration, this is a powerful agent of change.

    No doubts about that. Who has ever doubted that proteins change? Of course they change. RV is a powerful agent of change. NS is a minimally powerful agent of fixation of functional change. And so?

    Change is not functional information. Funtional information is what we have ot explain, not change.

    By the way, those “powerful agents of change” are exactly the reason why we can use conservation through long evolutionary times (the strange fact that there are complex things that do not change), as a reliable measure of functional constraints, IOWs functional complexity.

    But I do think that selection conserves proteins with the best function.

    Of course it does, It’s called negative, or purifying, selection. Which is a very powerful agent to preserve what is already functional.

    And so why shouldn’t proteins that do the best job be retained both by modern E. coli and humans.

    Of course they should be retained. And they are retained. That’s not the problem.

    The problem is: how did they reach the state where they do the best job? Or, more precisely, the state where they simply do the job? Again, think of the F1 subunit of ATP synthase as a reference example.

    Oh, I realise the depth and breadth of the problem that biologists have in explaining everything biological.

    Me too.

    But the same explanation fits the facts.

    I may be distracted, but I have seen no “explanation” in the things you say. Least of all an explanation that “fits the facts”. I must be very, very distracted.

    And ID does not have an alternative explanation. At. All.

    So are you denying that conscious design can easily generate complex functional information? That it is the only known part of reality that can do that?

    Counter-examples, please?

  366. 366
    PavelU says:

    346 Antonin:

    “Oh and thanks to PavelU for the link.”

    You’re very welcome!

    Did you understand it? Do you agree that it’s a strong argument?

    -PU

  367. 367
    PeterA says:

    gpuccio @364:

    “Change is not functional information. Functional information is what we have to explain, not change.”

    Now, let’s hope your interlocutors get the point. Sometimes it takes time… 🙂

  368. 368
    PeterA says:

    PavelU @365:

    “Do you agree that it’s a strong argument?”

    A strong argument for what? For boring fairy tales?

  369. 369
    Antonin says:

    Jawa, PavelU, OLV and PeterA? Commonly descended from dionisio? Just askin! 🙂

  370. 370
    EugeneS says:

    Nonlin

    “Entropy is used both in thermodynamic systems and information theory (aka data transmission) courtesy of Claude E. Shannon.”

    It should not be a surprise to you that the two notions, thermodynamic entropy and information entropy, are closely related and, broadly speaking, are the same thing.

  371. 371
    EugeneS says:

    GP,

    Many Thanks! I always enjoy reading your contributions 🙂

  372. 372
    PeterA says:

    gpuccio @364:

    “The problem is: how did they reach the state where they do the best job? Or, more precisely, the state where they simply do the job? Again, think of the F1 subunit of ATP synthase as a reference example.”

    That’s a question to answer. Can Antonin answer it?

    “I may be distracted, but I have seen no “explanation” in the things you say. Least of all an explanation that “fits the facts”. I must be very, very distracted.”

    I missed that “explanation” too.
    Join the “distracted” club! 🙂

  373. 373
    gpuccio says:

    EugeneS, PeterA:

    Thank you, guys. Your appreciation is very much appreciated! 🙂

  374. 374
    Antonin says:

    …your interlocutors…

    🙂

  375. 375
    Antonin says:

    gpuccio:

    I don’t discuss reli[gi]ous arguments here.

    I’m not asking you to. Some of our polite interlocutors were wondering about me, so I’m just making my own religious stance clear again.

  376. 376
    Mung says:

    Antonin:

    See the difference?

    No I don’t. They are both binary. The molecules bind or they don’t, the key opens the lock or it doesn’t.

    A key can open more than one lock, it’s not an all or nothing proposition as you are trying to make it.

    I can see that sensible discussion with you is unlikely.

    LoL.

  377. 377
    Antonin says:

    Gpuccio, responding to Antonin;

    Yet we have a mechanism that can explain many of these events.

    Of course. It’s design.

    Back to the impasse. On a religious and philosophical level, to some extent I agree with you (and on much else, if we were to compare notes – but that would be boring). But you are claiming to have a scientific argument, if I understand you. I repeat, until “design” becomes more than the utterance of the mantra, until you have a hypothesis, a mechanism, you have nothing to offer the scientific community. I’m reminded of Richard Feynman’s phrase: “cargo cult science”.

    I’d still like to hear when someone is able to propose a positive claim that would validate “Intelligent Design” as a genuine alternative to evolutionary theory. That initial testable hypothesis, perhaps.

  378. 378
    Antonin says:

    In the meantime maybe mung will be able to pass on your “thief” scenario for Joe Felsenstein to consider.

  379. 379
    Antonin says:

    Mung:

    They are both binary.

    Nope. Attraction/repulsion between molecules is not binary. Enzyme/substrate bonding is measurable and variable.

  380. 380
    Antonin says:

    @ mung

    What are the chances of you passing on Gpuccio’s request that Joe Felsenstein take a look at his “thief” scenario?

  381. 381
    kairosfocus says:

    ES,

    Yes. While we could elaborate, I find the following Wiki clip helpful — not least due to the admission against ideological interest angle:

    At an everyday practical level the links between information entropy and thermodynamic entropy are not close. Physicists and chemists are apt to be more interested in changes in entropy as a system spontaneously evolves away from its initial conditions, in accordance with the second law of thermodynamics, rather than an unchanging probability distribution. And, as the numerical smallness of Boltzmann’s constant kB indicates, the changes in S / kB for even minute amounts of substances in chemical and physical processes represent amounts of entropy which are so large as to be right off the scale compared to anything seen in data compression or signal processing.

    But, at a multidisciplinary level, connections can be made between thermodynamic and informational entropy, although it took many years in the development of the theories of statistical mechanics and information theory to make the relationship fully apparent. In fact, in the view of Jaynes (1957), thermodynamics should be seen as an application of Shannon’s information theory: the thermodynamic entropy is interpreted as being an estimate of the amount of further Shannon information needed to define the detailed microscopic state of the system, that remains uncommunicated by a description solely in terms of the macroscopic variables of classical thermodynamics. For example, adding heat to a system increases its thermodynamic entropy because it increases the number of possible microscopic states that it could be in, thus making any complete state description longer. (See article: maximum entropy thermodynamics.[Also,another article remarks: >>in the words of G. N. Lewis writing about chemical entropy in 1930, “Gain in entropy always means loss of information, and nothing more” . . . in the discrete case using base two logarithms, the reduced Gibbs entropy is equal to the minimum number of yes/no questions that need to be answered in order to fully specify the microstate, given that we know the macrostate.>>]) Maxwell’s demon can (hypothetically) reduce the thermodynamic entropy of a system by using information about the states of individual molecules; but, as Landauer (from 1961) and co-workers have shown, to function the demon himself must increase thermodynamic entropy in the process, by at least the amount of Shannon information he proposes to first acquire and store; and so the total entropy does not decrease (which resolves the paradox).

    KF

    PS: An interesting remark on zeroth law and cosmos as a whole. You know I deeply respect the Russian work and books. BTW I recently rejoiced to find Savelyev’s 3-vol Gen Physics at I think it was Web Archive. Excellent survey.

  382. 382
    kairosfocus says:

    Antonin, a process has been put on the table for relevant design, with examples starting with Venter et al. Intelligent action works by conscious intent, knowledge and skill, not blind mechanism. This, we all know and can readily observe. As I have pointed out the distinction between intelligent signal and mindless noise is right in the heart of communication and information theory. Computer science is a related field where intelligent action is routinely integrated into the science. Design inferences on tested, reliable signs are routine in many pure and applied scientific fields; it is only the shadow cast by materialistic ideology that tries to lock it out of origins studies. That ideological lockout has reached a pitch where something as routinely observable as functionally specific, configuration based complex organisation and associated information is viewed with hyperskeptical dismissal. FYI, the text in your comments is a case in point, and it was created by your intelligently directed configuration. Similar s-t-r-i-n-g data structures are found in D/RNA, exhibiting similar alphanumeric code, used in algorithmic processes such as protein assembly. There is additional deep knowledge implied by the fold, agglomerate, modify, function processes that set up proteins, also. KF

  383. 383
    Silver Asiatic says:

    Antonin

    I’m Catholic. I believe in the Creation.

    The Creation is that God created something. That’s a form of creationism.

    What do you think God created? How do you support your belief in that?

  384. 384
    Mung says:

    Antonin:

    What are the chances of you passing on Gpuccio’s request that Joe Felsenstein take a look at his “thief” scenario?

    Zero. Is that binary enough for you?

    Attraction/repulsion between molecules is not binary.

    Neither is the fit between a key and a lock. You obviously know nothing about auto theft.

  385. 385

    There’s no language involved in protein synthesis.

    In 1946, John Von Neumann (building on Alan Turing’s machine from 1938) famously predicted the physical and organizational requirements of an autonomous self-replicator. Those requirements included a high-capacity (sequential, multi-referent) symbol system for memory, as well as a set of Peircean interpretants to establish function. That prediction was experimentally validated a few years later by Crick, Watson, Hoagland, Zamecnik, Nirenberg, Matthaei, and others.

    Since that time, starting about half a century ago, the required language structure in the gene system was carefully described (as such) within the physics literature by Howard Pattee and others. This was done without even a hiccup, given the simple fact that the critical observables aren’t even in question. This also includes the semantic closure required for the origin of the system (echoing Von Neumann’s “threshold of complexity” from his original prediction).

    You’ve provided nothing to refute any of these things, nor has anyone else at any lab or institution anywhere on the planet; and certainly no one has even come close to demonstrating a viable pathway to the required semantic closure.

    Your claim that there is ‘no language in protein synthesis’ may serve a rhetorical purpose, but it is uninformed, and can only serve its purpose by first ignoring the (well-documented) organizational requirements of the system. It is also not surprising that you suggest ID has no mechanism to introduce design into the stochastic environment, then you turn around and quietly assume that very mechanism in your preferred explanation.

  386. 386

    Hello DATCG! at #230

    I am in and out here recently; my household has been mandatorily evacuated from recent flooding, and we are only now trying to put things back together again. All is good. I check in when I can. 🙂 🙂

  387. 387
    EricMH says:

    @UB, glad you are ok!

  388. 388
    EricMH says:

    All, I’ve lost track of the current conversation here.

    But, for those still interested in the OP, here is a formal proof that halting oracles (i.e. intelligent agency) can break the law of information non growth:

    https://www.am-nat.org/site/law-of-information-non-growth/

    I also have a short explanation of why this matters empirically:

    https://www.am-nat.org/site/halting-oracles-as-intelligent-agents/

    So, more demonstration that ID fits easily within mainstream info theory and computer science concepts.

  389. 389
    gpuccio says:

    EricMH:

    I absolute agree with you that halting oracles (i.e. intelligent agency) can explain complex function (which is more or less the same, I believe, as “breaking the law of information non growth).

    I see that you take the concept from Johnathan Bartlett. I read his article about that long time ago, and I found it really illuminating.

    From my point of view, it’s the conscious experience of meaning and purpose that allows consciousness to act as an intuitive “oracle”. That intuitive source makes all the difference.

  390. 390
    EricMH says:

    @gpuccio, yes exactly. The proof essentially shows that halting oracles can create information, unlike natural processes. Jonathan is a brilliant man.

    And, to continue beating the dead horse, this is all clearly demonstrable within standard information theory and computer science. There is nothing controversial regarding ID’s theoretical claims.

    The supposed controversy raised when Dembski first published his work is without merit. It is also highly questionable, since I find it hard to believe the information theory experts were unaware of the theorems I point out, nor aware of the implications.

  391. 391
    gpuccio says:

    UB:

    I hope everything is fine now.

    We had some floods here in Italy too, in these days.

    Always good to hear from you! 🙂

  392. 392
    kairosfocus says:

    UB, Antonin obviously disagrees with Crick, as was repeatedly pointed out above. Apparently he refuses to acknowledge that the genetic code is a code, which is inherently an expression of language. Evidently, he is unaware that the anticodons on the tRNA (which respond to the prong-height codons in mRNA transcribed from DNA) are on the opposite end of the folded tRNA from the AA-bearing CCA tool tip. Worse, that due to that universal socket as tool tip, it is the loading enzyme that effects the coded assignment of a given AA to a given tRNA, using general conformation. That is, it is not determined by Chemistry, given the common CCA socket at the tool tip end. He further refuses to acknowledge that there is a start, stepwise elongation and stop, with the particular sequence of AA’s being chained set up so that the resulting polymer will fold, agglomerate, take additional elements and fit key-lock style to function. This rhetorical pattern of dismissing material and reasonably established facts and meanings shows that the inference from such to design is so strong that the ideology that rejects is forced to obfuscate and resort to denial and dismissal. Sadly telling. KF

  393. 393
    kairosfocus says:

    PS: Trust all is well, post floods — now I see that. Here, we just had a vote of no confidence in Assembly, which failed.

  394. 394
    kairosfocus says:

    GP, floods near you? How are you doing? KF

  395. 395
    gpuccio says:

    KF:

    Well, thank you. No personal involvment, but there were some deaths even here in the south, and that is rather unusual.

  396. 396
    Bob O'H says:

    Eric @ 387 –

    Using the observation that more information cannot increase uncertainty,

    For Bayesians it certainly can (in the sense that adding data can increase the variance of a posterior distribution). So is this a claim made in a more specific context? I’m not saying it’s wrong, just it’s not universally true.

  397. 397
    jawa says:

    KF @391:
    Well stated. Thanks.

  398. 398
    jawa says:

    Glad to read that UB and GP weren’t badly affected by the mentioned floods.

  399. 399
    kairosfocus says:

    GP, ouch, sympathies but glad to see you are well. KF

  400. 400
    kairosfocus says:

    BO’H: In information systems, added information — as opposed to noise — as a rule reduces uncertainty as to the state of its source. In the Bayesian case you mention, the underlying uncertainty of the distribution was changed or updated or corrected, thus more information gives a higher (and presumably better warranted) value. KF

  401. 401
    Bob O'H says:

    kf – Even when “as a rule” things happen, there can be exceptions. Eric was claiming that something happened without exception. But as a general statement that is false. So I assume it’s a more specific statement, so I’d just like to know what the specific conditions are.

  402. 402
    EricMH says:

    @Bob O’H,

    In Kolmogorov complexity, if the input bitstring doesn’t tell us anything about the bitstring we are trying to compress, we just ignore it and generate the normal compression. So, more information (bitstrings) can never increase the compression length of the target bitstring.

  403. 403
    kairosfocus says:

    BO’H: I used the basic info theory definition of information, which is part of how it is quantified. The point is, you are at the receiving end of a noisy channel in general, and need to estimate the message sent; where also source, transmitter and receiver are in general infected with that bane of communication, noise. More information in your case led to a corrected (or at least updated), less uncertain estimate of variance; that is, it reduced uncertainty as to a certain statistical parameter relevant to the source and its messages. Per your hyp, the further information increased its value. Then, it so happens that variance in statistics has to do with the degree of scatter in a population and so a higher and more likely correct estimate of variance corresponds to higher uncertainty about the source and its messages in a different sense, a statistical one. We therefore have to distinguish two contexts that are at work in different aspects of the situation. KF

  404. 404
    kairosfocus says:

    PS: This intro & summary by Wikipedia (speaking against known ideological agenda) may help:

    Information is any entity or form that provides the answer to a question of some kind or resolves uncertainty. It is thus related to data and knowledge, as data represents values attributed to parameters, and knowledge signifies understanding of real things or abstract concepts.[1] As it regards data, the information’s existence is not necessarily coupled to an observer (it exists beyond an event horizon, for example), while in the case of knowledge, the information requires a cognitive observer.

    Information is conveyed either as the content of a message or through direct or indirect observation. That which is perceived can be construed as a message in its own right, and in that sense, information is always conveyed as the content of a message.

    Information can be encoded into various forms for transmission and interpretation (for example, information may be encoded into a sequence of signs, or transmitted via a signal). It can also be encrypted for safe storage and communication.

    Information reduces uncertainty. The uncertainty of an event is measured by its probability of occurrence and is inversely proportional to that. The more uncertain an event, the more information is required to resolve uncertainty of that event. The bit is a typical unit of information, but other units such as the nat may be used. For example, the information encoded in one “fair” coin flip is log2(2/1) = 1 bit, and in two fair coin flips is log2(4/1) = 2 bits.

    The concept that information is the message has different meanings in different contexts.[2] Thus the concept of information becomes closely related to notions of constraint, communication, control, data, form, education, knowledge, meaning, understanding, mental stimuli, pattern, perception, representation, and entropy.

    PPS: My longstanding discussion in Sec A of my always linked note (click my handle) may also be helpful.

  405. 405
    kairosfocus says:

    PPS: It being a rather rainy morning, let me pause and clip from the note:

    The second major step is to refine our thoughts, through discussing the communication theory definition of and its approach to measuring information. A good place to begin this is with British Communication theory expert F. R Connor, who gives us an excellent “definition by discussion” of what information is:

    From a human point of view the word ‘communication’ conveys the idea of one person talking or writing to another in words or messages . . . through the use of words derived from an alphabet [NB: he here means, a “vocabulary” of possible signals]. Not all words are used all the time and this implies that there is a minimum number which could enable communication to be possible. In order to communicate, it is necessary to transfer information to another person, or more objectively, between men or machines.

    This naturally leads to the definition of the word ‘information’, and from a communication point of view it does not have its usual everyday meaning. Information is not what is actually in a message but what could constitute a message. The word could implies a statistical definition in that it involves some selection of the various possible messages. The important quantity is not the actual information content of the message but rather its possible information content.

    This is the quantitative definition of information and so it is measured in terms of the number of selections that could be made. Hartley was the first to suggest a logarithmic unit . . . and this is given in terms of a message probability. [p. 79, Signals, Edward Arnold. 1972 . . . Apart from the justly classical status of Connor’s series, his classic work dating from before the ID controversy arose is deliberately cited, to give us an indisputably objective benchmark.]

    To quantify the above definition of what is perhaps best descriptively termed information-carrying capacity, but has long been simply termed information (in the “Shannon sense” – never mind his disclaimers . . .), let us consider a source that emits symbols from a vocabulary: s1,s2, s3, . . . sn, with probabilities p1, p2, p3, . . . pn. That is, in a “typical” long string of symbols, of size M [say this web page], the average number that are some sj, J, will be such that the ratio J/M –> pj, and in the limit attains equality. We term pj the a priori — before the fact — probability of symbol sj. Then, when a receiver detects sj, the question arises as to whether this was sent. [That is, the mixing in of noise means that received messages are prone to misidentification.] If on average, sj will be detected correctly a fraction, dj of the time, the a posteriori — after the fact — probability of sj is by a similar calculation, dj. So, we now define the information content of symbol sj as, in effect how much it surprises us on average when it shows up in our receiver:

    I = log [dj/pj], in bits [if the log is base 2, log2] . . . Eqn 1

    This immediately means that the question of receiving information arises AFTER an apparent symbol sj has been detected and decoded. That is, the issue of information inherently implies an inference to having received an intentional signal in the face of the possibility that noise could be present. Second, logs are used in the definition of I, as they give an additive property: for, the amount of information in independent signals, si + sj, using the above definition, is such that:

    I total = Ii + Ij . . . Eqn 2

    For example, assume that dj for the moment is 1, i.e. we have a noiseless channel so what is transmitted is just what is received. Then, the information in sj is:

    I = log [1/pj] = – log pj . . . Eqn 3

    This case illustrates the additive property as well, assuming that symbols si and sj are independent. That means that the probability of receiving both messages is the product of the probability of the individual messages (pi *pj); so:

    Itot = log1/(pi *pj) = [-log pi] + [-log pj] = Ii + Ij . . . Eqn 4

    So if there are two symbols, say 1 and 0, and each has probability 0.5, then for each, I is – log [1/2], on a base of 2, which is 1 bit. (If the symbols were not equiprobable, the less probable binary digit-state would convey more than, and the more probable, less than, one bit of information. Moving over to English text, we can easily see that E is as a rule far more probable than X, and that Q is most often followed by U. So, X conveys more information than E, and U conveys very little, though it is useful as redundancy, which gives us a chance to catch errors and fix them: if we see “wueen” it is most likely to have been “queen.”)

    Further to this, we may average the information per symbol in the communication system thusly (giving in termns of -H to make the additive relationships clearer):

    – H = p1 log p1 + p2 log p2 + . . . + pn log pn

    or, H = – SUM [pi log pi] . . . Eqn 5

    H, the average information per symbol transmitted [usually, measured as: bits/symbol], is often termed the Entropy; first, historically, because it resembles one of the expressions for entropy in statistical thermodynamics. As Connor notes: “it is often referred to as the entropy of the source.” [p.81]

    –> Notice, how additional information reduces uncertainty as to the source’s state and message.

  406. 406
    Bob O'H says:

    Eric @ 401 – Ah, thanks. That’s a very specific use of the term!

  407. 407
    EricMH says:

    @Bob O’H, yes I should probably change the wording. Referring to “uncertainty” is probably not helpful in that context.

  408. 408
    Mung says:

    kairosfocus:

    A good place to begin this is with British Communication theory expert F. R Connor, who gives us an excellent “definition by discussion” of what information is

    Hi kf, does this come from a book that you have?

  409. 409
    kairosfocus says:

    Yup, have had it for 37 years now; part of a series of short textbooks.

  410. 410
  411. 411
    EricMH says:

    @KF, thanks for the quote. This clarifies the issue for the infotropy crowd:

    > The important quantity is not the actual information content of the message but rather its possible information content.

  412. 412
    kairosfocus says:

    EMH, yup. Also see the Wiki clip on info and entropy. KF

  413. 413
    kairosfocus says:

    chirp chirp chirp

  414. 414
    Mung says:

    kf:

    chirp chirp chirp

    ok, i disagree with Eric. heh.

    The important quantity is not the actual information content of the message but rather its possible information content.

    Why is the possible information content of the message the important quantity when Shannon Information has nothing to do with the “information carry capacity” of a message but rather with the information carrying capacity of a communications channel?

    IOW, it is concerned not with what’s in a message but rather with the set of possible messages that may be sent -> encoded -> transmitted -> decoded -> received.

    How do we calculate the “information carrying capacity” of “the message” anyways?

  415. 415
    Mung says:

    Mung’s First Law of Information Theory:

    The important quantity is not information content of the message, but rather the entropy of the source.

  416. 416
    ET says:

    Antonin:

    I’d still like to hear when someone is able to propose a positive claim that would validate “Intelligent Design” as a genuine alternative to evolutionary theory.

    There isn’t any scientific theory of evolution. The real question is “is there a scientifically valid alternative to ID?”- and the answer is “No”.

    But anyway- ID is based on three premises and the inference that follows (DeWolf et al., Darwinism, Design and Public Education, pg. 92):

    1) High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.

    2) Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.

    3) Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.

    4) Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.

    Those are the core concepts of ID and to falsify Intelligent Design all one has to do is demonstrate that natural selection can produce irreducibly complex biological systems.

  417. 417
    ET says:

    Antonin:

    I doubt I’m alone in concluding exchanging comments with you is not productive.

    Your projection is duly noted as exchanging comments with you is useless. All I am doing is pointing out your willful ignorance.

    I see you made no attempt to support your ludicrous claim regarding “disproving” Felsenstein.

    YOU have made no attempt to support anything Joe F has ever said in criticizing ID. You have absolutely no clue at all. Clearly you are just a willfully ignorant troll.

  418. 418
    ET says:

    Antonin:

    Koonin suggests several scenarios where evolution from simpler codes could have occured.

    And until he tests his hypothesis it remains outside of science. Clearly science is not your forte or else you would have known that.

    And it is far from certain that proteins were required for the earliest forms of life.

    There isn’t any evidence to the contrary. Your wishful thinking doesn’t help

    RNA has catalytic ability, even conserved in the ribosome today.

    So what? Spiegelman’s monster crushes the hoped for RNA world.

  419. 419
    ET says:

    Antonin (on common design):

    Until you or anyone propose a mechanism, …

    Design is a mechanism. Buy a dictionary and learn how to use it.

    Common design is an observed phenomena. We see it in houses, computers, automobiles- well all throughout technology. It doesn’t make any sense from a design perspective to keep designing things when you already have available materials to work with.

  420. 420
  421. 421
    EricMH says:

    @Mung what is a probability distribution?

  422. 422
    kairosfocus says:

    Mung, if a certain “symbol” MUST be transmitted [= no contingency], there is no information. If there are several or many possibilities [high contingency], learning that say option_j of n happened is informational. Source entropy as Connor notes, is avg info per symbol. Just to be clear, 2 options, equiprobable is 1 bit per symbol. 20 equiprobable options gives 4.32 bits per symbol. Real codes are never exactly equiprobable, and those that are more likely are less informational than those that are less likely. Consider English text has e perhaps 1/8 of the time, but x is far less likely in typical text (Algebra books need not apply). KF

  423. 423
    ET says:

    The following may be helpful- Information Is Not Entropy, Information Is Not Uncertainty!:

    “Information is always a measure of the decrease of uncertainty at a receiver (or molecular machine).”

  424. 424
    jawa says:

    KF @422,
    Clear explanation. Thanks.

  425. 425
    jawa says:

    ET @419:

    For example, OOP in software development is common design.

    Certain analogy between OOP and biological systems is obvious to any open-minded observer.

  426. 426
    gpuccio says:

    ET:

    OK, I had my good laugh! 🙂

    Of course, a symbolic code is a mapping that is arbitrary, and does not depend in any way on necessity laws.

    Both spectral bands and tree rings are clear examples of patterns generated by necessity laws. There is no arbitrary mapping in them. Thefore, they are in no way symbolic codes.

    There exists no necessity law that can encode information about protein sequences into nucleotide sequences by the symbolic genetic code.

  427. 427
    gpuccio says:

    jawa:

    “Certain analogy between OOP and biological systems is obvious to any open-minded observer.”

    Of course. Biological programs are, in most cases, object oriented.

  428. 428
    EricMH says:

    @ET, great article!

  429. 429
    kairosfocus says:

    ET, Information is not thermodynamic entropy but for cause there is an informational school of thought, see Sec A in my linked through my handle. Entropy measures the avg missing info to specify particular microstate given macro-level state. Note: a great many microstates will be compatible with a given macrostate. This ties the two domains together. KF

  430. 430
    Mung says:

    EricMH:

    @Mung what is a probability distribution?

    I give up. A distribution of probabilities? 🙂

    I seem to recall reading something about how a probability distribution is defined, I’ll see if i can find it.

  431. 431
    Mung says:

    Add to be agreeing with Schneider about anything. 🙂

  432. 432
    Antonin says:

    Mung

    Antonin:

    What are the chances of you passing on Gpuccio’s request that Joe Felsenstein take a look at his “thief” scenario?

    Zero. Is that binary enough for you?

    Does sort of suggest you agree with me that gpuccio hasn’t really got much of an argument. I’ve been reading The Skeptical Zone recently. You seem to be a different person there.

    Attraction/repulsion between molecules is not binary.

    Neither is the fit between a key and a lock. You obviously know nothing about auto theft.

    Very droll.

  433. 433
    Antonin says:

    Upright Biped:

    Your claim that there is ‘no language in protein synthesis’ may serve a rhetorical purpose…

    It’s a simple statement of fact. It's all chemistry.

  434. 434
    gpuccio says:

    Antonin:

    The mapping of AAs to codons is symbolic. It has nothing to do with chemistry.

  435. 435
    gpuccio says:

    Antonin:

    I would never pass that request to Joe Felsestein. I never force people to answer my points.

    Does that “suggest I agree with you that I haven’t really got much of an argument”?

    Just to know.

  436. 436
    Nonlin.org says:

    gpuccio @313,

    You say: “Nonlin says that my arguments are unconvincing. Facing such strict counter-logic, I will certainly have to change my mind.”

    Much more than “unconvincing”. Proven wrong.
    As the sage said:
    “Of course, if I am a smart chinese. I could perhaps make a design inference for the sonnet just the same, because we know that some linguistic patterns can be recognized even if we don’t understand the meaning.”

  437. 437
    Nonlin.org says:

    KF @318

    What about “cell based life”?
    The topic is Design. Much broader.

    Wow! 400+ comments for something as clear and simple as Design? This is getting ridiculous.

  438. 438
    ET says:

    Antonin on protein synthesis:

    It’s all chemistry.

    Except for the genetic code which isn’t all chemistry.

  439. 439
    Nonlin.org says:

    EugeneS @370

    You say: “It should not be a surprise to you that the two notions, thermodynamic entropy and information entropy, are closely related and, broadly speaking, are the same thing.”

    And your claim was “[entropy has] Nothing to do with data.”

    Your claim is wrong as shown here: https://en.wikipedia.org/wiki/Entropy_(information_theory)
    “the entropy of a fair coin toss is 1 bit, and the entropy of m tosses is m bits”.

    Obviously, by tossing coins we generate Data, but not Information. If you insist otherwise, explain what information you get from coin tossing all day long.

  440. 440
    gpuccio says:

    Nonlin.org:

    You are really unbearable.

    Of course there are some patterns in language that can be, sometimes, recognized even if we don’t understand the language. That will be enough to infer design sometimes, other times it will not.

    But of course, if we understand the meaning, the design inference is immensely easier and stronger. That does not depend on patterns or order.

    I am tired of your false reasonings. Really, if you have no ability to reason correctly, you should stop wasting the time of others.

  441. 441
    kairosfocus says:

    Antonin, with all respect, it seems your quarrel is with Crick et al (and the Nobel Prize Committee), not merely UD. That has been repeatedly pointed out to you, there is a reason that a genetic code has been identified and is now routinely used. What you have managed to do is to inadvertently show the strength of the point by your rhetorical device of repeating a long since corrected error as though it deflects the force of the point. KF

  442. 442
    kairosfocus says:

    Nonlin, yes, there is in info theory something called the entropy of a source, which boils down to the weighted average information per symbol; as I summarised above. What it means and how that is tied to the mathematically similar value in statistical thermodynamics is NOT a trivial exercise. There is indeed a connexion (albeit still contended against), as I pointed out above; discussed in Sec A as is linked through my handle. In a nutshell, the statistical thermodynamic entropy can be seen as average missing information to specify the particular microstate of an entity, given that its macro-level state has been characterised by a suitable set of lab scale state variables such as P, V, T etc. This is because there are as a rule a great many possible microscopic configurations associated with such a macrostate. The value can be quantified based on some description language and string of Y/N q’s, up to a suitable constant of proportionality. This last is where for instance, Boltzmann’s k plays such a role in his classic work. Much of the underlying work was done by Jaynes et al, and I point to and cite Harry Robertson’s summary in my linked. KF

  443. 443
    kairosfocus says:

    PS: Nonlin, cell based life is a decisive test case on inferring design on well known, readily accessible evidence. What we see above is that in cases, objectors are willing to dismiss the reality and significance of the genetic code. Codes, here, being expressions of language used cybernetically through molecular nanotechnology. That then points to the root problem, not the facts or the actual strength of the case but ideological domination. It is much like saying music and singing are not real because there is just physics of vibrations and waves there; refusing to acknowledge that the physical supports higher level interactions that manifest mind at work — in a sense, the crudest materialism much like saying there is no mind as brain cells and electrochemistry are at work in a network. But in the end, the sheer force of the case will prevail. Notwithstanding, if the import of the cell using coded algorithmic information with start, stepwise procedure and halting is brushed aside, things like fine tuning will be and even moreso, abstract general discussions on design inferences and on algorithmic compressibility. All of this is a sad indictment of our self-destructive, dying civilisation.

  444. 444
    Antonin says:

    I would never pass that request to Joe Felsestein. I never force people to answer my points.

    Does that “suggest I agree with you that I haven’t really got much of an argument”?

    Just to know.

    Yes as a matter of fact. And giving someone a heads-up is hardly applying force. I thought you were interested in Felsenstein’s thoughts on your thief scenario.

  445. 445
    Antonin says:

    The mapping of AAs to codons is symbolic. It has nothing to do with chemistry.

    Nothing to do with chemistry? Good grief! This is where taking analogies to extremes gets you. I beg you, gpuccio, turn back from the dark side.

  446. 446

    During translation, the codon-to-anticodon association is chemically independent of anticodon-to-amino acid association. This is the observed fact of the matter. I think we all now see that such facts do not interest you, and that you will not respond to them, but they remain just the same.

  447. 447
    kairosfocus says:

    UB, facts are stubborn things, but if someone is determined not to acknowledge them, he will not yield to mere facts. Recall, above I took time to point out above that the anticodon and the universal joint CCA- tool tip that holds the AA on a tRNA are at opposite ends of the folded tRNA. That alone should be a big clue, as the chemistry to bond any given AA to a tRNA is the same and the anti-codon is not right there to have an effect. KF

  448. 448
    ET says:

    Earth to Antonin- If you think the mapping of amino acids to codons is all about chemistry then by all means make your case or shut up.

    Or do you really think that your snark remarks are an actual argument?

  449. 449
    EricMH says:

    @Mung, I would say a probability distribution counts how many options are available.

    Say we have a bag with 1 green marble and 1 red marble. The probability of drawing a red marble is 1/2, which is 1 divided by the number of options.

    If there are 2 green marbles and 1 red marble, then the probability of drawing red becomes 1/3, which is still 1 divided by the number of options.

    However, the probability for drawing a green marble is 2/3. Where did the 2 come from? Doesn’t that contradict 1 divided by number of options? It is because we group and add all the 1/3s for the green marbles, so still consistent with counting the number of options.

    What do you think?

  450. 450
    Mung says:

    Upright BiPed:

    During translation, the codon-to-anticodon association is chemically independent of anticodon-to-amino acid association. This is the observed fact of the matter.

    And in fact it must be that way. Does information theory shed any light on why it must be that way? I suspect that it may.

  451. 451
    Mung says:

    @EricMH,

    I received Kolmogorov’s book Foundations of the Theory of Probability yesterday and was hoping to find an answer in it but I had difficulty reading the notation he uses. 🙂

    Have you seen this book?

    Information and Randomness: An Algorithmic Perspective

  452. 452
    kairosfocus says:

    EMH and Mung, a probability distribution for some variable quantity x, indicates the range of values and the relative likelihood that the variable will take particular values. A fair six-sided die will have one of {1, 2 . . . 6} uppermost and each is equiprobable, i.e. “flat.” If the die is loaded so say it now reads 6 90% of the time and the other five values 2% each, it will now have a J-distribution (or perhaps, reverse-L is a better description). If the variable follows the Gaussian pattern, its relative frequency of possible values follow a bell curve. The Quincunx/ Galton Board model illustrates how: https://www.youtube.com/watch?v=AUSKTk9ENzg KF

  453. 453
    Antonin says:

    During translation, the codon-to-anticodon association is chemically independent of anticodon-to-amino acid association.

    What I suspect you are objecting to is the evolvability of the current process from simpler precursors. What we can observe is how living organisms currently surviving on Earth manage their biochemistry. We can only surmise what the biochemistry was like in the earliest organisms that could both grow and replicate. It’s an interesting fact that aminoacyl tRNA synthetases have an arbitrary associative link between codon and amino acid residue. This is the observed fact of the matter but not fatal to evolutionary theory

    I think we all now see that such facts do not interest you…

    You are mistaken. The question of how the basic biochemical pathways essential to life evolved from simpler precursors is challenging with no direct evidence to work with. It’s an active field for hypothesis construction.

    …and that you will not respond to them…

    Insofar as I am able, I’m a layman with regard to biochemistry and proposed evolutionary pathways (A simpler doublet code, a smaller suite of amino acids, RNA as precursor for both heritable storage and catalysis) but I try to keep myself informed on progress and new ideas.

    …but they remain just the same.

    Do you, as a layman, keep up with progress in the field? What do you consider a problem for evolution with respect to biochemistry of the chain of living organisms from the first life to today?

    Michael Behe is a biochemist sympathetic to “Design”. Have you run your ideas past him?

  454. 454
    kairosfocus says:

    Antonin, can you at least acknowledge that the CCA- universal joint that attaches the AA is at the opposite end of the anticodon triplet that locks to the mRNA codon in the ribosome as proteins are made? That, therefore the AA put on a given tRNA is not chemically determined? That, the codon-anticodon match is physically separated from the action that clicks an AA to the emerging protein? That, the tRNAs are loaded by enzymes that sense overall conformation not simply anticodon? Thus, that the chaining of a protein is based on the genetic code and the high contingency along a D/RNA chain, and that protein functionality is separated from the high contingency of chaining possibilities? That, that functionality depends on picking chaining patterns which come from thousands of deeply isolated domains in AA sequence space? And more? KF

  455. 455
    Mung says:

    Antonin:

    This is the observed fact of the matter but not fatal to evolutionary theory

    Of course not. It’s what is required for evolution to occur in the first place. It’s a pre-requisite.

  456. 456
    jawa says:

    Mung,

    Nothing is fatal to something that is not alive. 🙂

  457. 457
    EricMH says:

    @KF defining a probability distribution in terms of probabilities seems circular. What is a probability? I think it is 1 / number of options, like marbles in a bag.

  458. 458
    Antonin says:

    KF:

    Antonin, can you at least acknowledge that the CCA- universal joint that attaches the AA is at the opposite end of the anticodon triplet that locks to the mRNA codon in the ribosome as proteins are made?

    Yes.

    That, therefore the AA put on a given tRNA is not chemically determined?

    No. (non sequitur)

  459. 459
    Antonin says:

    That, that functionality depends on picking chaining patterns which come from thousands of deeply isolated domains in AA sequence space?

    No. Unsupported assertion.

  460. 460
    kairosfocus says:

    EMH, the emphasis falls on the distribution aspect. Probabilities are what the distribution distributes. As for defining a probability, that is an exercise in itself in Mathematics and philosophy. In a situation where there are contingencies such that under similar circumstances diverse outcomes are possible, we may then ask whether there is any reason some are more or less likely; often adjudged on relative frequencies as observed or perceived. If not, we apply indifference yielding the sort of 1/n ratio for n possibilities. Where there is reason to view some as more or less likely, then the sum of likelihoods is re-balanced to reflect such, while overall we still sum to 1. Then, we can add endpoints, where something may never happen, the zero, or something must happen, the 1. Onward, we move to the continuous random variable, where then finite values obtain for ranges within the span of possibilities. Obviously, there is more but this is enough to see how we are setting up an abstract model-world with structural and quantitative features. KF

  461. 461
    kairosfocus says:

    Antonin, it seems you have homework to do to see what is actually supported. You at least acknowledge the basic fact of the folded tRNA, where anti-codons and CCA-tips are at opposite ends. The anti-codon does not determine the loading of the tRNA, it is not interacting by forming bonds with the AA. The universality of the CCA- tip means that the chemistry of bonding to the AA does not differ across the 20 tRNA’s of main interest. It is not an it fails to follow to note this and its import: the same CCA- tip can bond to 20 diverse AA’s (and IIRC artificial ones have been added). The isolation of protein fold domains in AA sequence space, the discovery of thousands of such, etc are facts on the ground. The functionality of a protein depends on how it folds, fits etc, and that is dependent on the codon sequence in mRNA, which is highly contingent; just ponder how for eukaryotes, there is post transcription editing. And so forth. Obviously, not just any AA sequence will function as a protein, and the distances in sequence space validate, isolated. KF

  462. 462
    gpuccio says:

    Antonin:

    From:

    “your approach is not persuasive”

    to:

    “Good grief!”

    your discussion is certainly gaining intensity, if not clarity and detail.

    Maybe you could explain to us fools what laws of chemistry explain the mapping of AAs to nucleotide codons in the translation system.

    And please, don’t say that Joe Felsestein can certainly do that better than you can. You have already exploited poor Joe enough in this discussion! 🙂

  463. 463
    gpuccio says:

    Antonin:

    The truth is very simple:

    There is no chemistry that can explain the mapping of AAs to codons of three nucleotides (IOWs, the genetic code).

    The mapping is implemented by the 20 aaRNA synthetases.

    Those 20 proteins are not a law of chemistry. They are specific machines that implement a task by their specific configuration.

    This is how the genetic code works, in all living beings.

    There is no explanation based on chemistry. The system works by a symbolic mapping, arbitrary and that has nothing to do with any laws of chemistry.

    If you disagree, please explain why. I am tired of your half statements and innuendos.

  464. 464
    EricMH says:

    @Mung & @KF the point I’m getting at is entropy measures the probability distribution, the probability distribution distributes probabilities, and probabilities are a count of options, and the options are possibilities. So, collapsing the chain shows entropy is just a measure of possibility, as these info theory quotes say.

    Pro evolution people want to say entropy is the same as information so that a random process can be said to generate information.

    However, entropy is just a measure of possible information, and so it doesn’t mean that everything produced by a high entropy source is actually information.

    This is a similar problem that people have with the concept of free will. Free will must be undetermined, but they equate undetermined and random, and randomness does not seem to be the same as free will. Thus, they conclude the will must be determined.

    But, there is a third option, where an object has high contingency, but is not random. This is what CSI measures. Thus, the acts of free will also have high contingency like a random process, but they are not random because they correlate with an independent target.

    So, if we go back to our high entropy source, its high entropy means it generates objects with high contingency. However, since high contingency is not coextensive with random, not all objects generated by the high entropy source necessarily fall in the same bucket. Some high contingency objects can fall in the random bucket, and other high contingency objects can fall in the CSI bucket, but the high entropy source does not predetermine which bucket the events fall into. The high entropy just means the source generates objects with high contingency, which is a necessary but not sufficient condition for CSI.

    Therefore, entropy is not the same as information, but information requires entropy.

  465. 465
    gpuccio says:

    EricMH at #464:

    Very good points! 🙂

    I believe that free will is one of the components that are exclusive to conscious experiences, and that explain CSI, especially in its functional form.

    The reasoning is simple:

    a) We have desires (a definite experience of our feeling inner space)

    b) We understand meanings: that helps us understand how our desires can be satisfied

    c) We have free will: we can initiate actions that are meant to satisfy our desires.

    One of the ways that such a sequence acts is in designing objects. As a result of that sequence of inner experiences, we create complex functional information in our consciousness, applying meaning to our desires, and then by our free will we implement that functional information into material objects, as a specific configuration meant to be functional to our desire.

    To do that, we use those rare high entropy and high contingency configurations that have the function we have envisioned.

  466. 466
    Antonin says:

    gpuccio:

    You have already exploited poor Joe enough in this discussion!

    How so? You mentioned him in connection with your thief scenario.

    Anyway, it appears that Professor Felsenstein has noticed this thread. He has posted at The Skeptical Zone and The Panda’s Thumb. In his post at The Skeptical Zone he says

    gpuccio also comments there trying to get someone to call my attention to an argument about Complex Functional Information that gpuccio made in the discussion of that earlier. I will try to post a response on that here soon, separate from this thread.

    link

  467. 467
    gpuccio says:

    Antonin:

    I mentioned Joe Felsestein about my thief scenario because that scenario was a criticism to a statement made by him.

    You, on the other hand, have said here, repeating a statement you had already mage in another thread:

    “Professor Felsenstein is a geneticist, specializing in population genetics, a mathematical approach to allele distribution. Of course he’s going to be able to more eloquently point out the flaws in your approach.”

    Why don’t you just try to “point out the flaws” in my approach yourself?

    OK, however, let’s wait for Joe Felsestein’s answer. I am really interested in it.

  468. 468
    gpuccio says:

    Antonin (and Joe Felsestein):

    By the way, just to be precise, I would like to clairfy that I have never “tried to get someone to call Joe Felsestein’s attention”. I have simply posted my old argument, specifying that it was a criticism to a statement by Joe Felsestein, and that, as far as I am aware, he has never answered that particular point. That’s all.

    Others, including you, have “tried to get someone to call JF”. Not me.

    But, of course, I will be happy if he answers my argument. 🙂

    By the way, JF’s statement was made at TSZ, and I quote it in my initial post about that issue, my comment #828 in the Ubiquitin thread:

    https://uncommondescent.com/intelligent-design/the-ubiquitin-system-functional-complexity-and-semiosis-joined-together/#comment-656019

    This is the original comment by JF, from TSZ:

    1. The 500 bits criterion, which originated with Dembski, was gpuccio’s criterion for “complex”, as I demonstrated in clear quotes from gpuccio in my previous comment.

    2. That counts up changes anywhere in the genome, as long as they contribute to the fitness, and it counts up whatever successive changes occur.

    3. Now, in both gpuccio’s and your comments, the requirement is added that all this occur in one protein, in one change, and that it be “new and original function”.

    4. That was not a part of the 500-bit criterion that gpuccio firmly declares to be the foundation of ID.

    5. There was supposed to be some reason why a 500 bit increase in functional information was not attainable by natural selection. Without any requirement that it involve “new and original function”.

    So what is the “foundational” requirement? A 500-bit increase in functional information, taken over multiple changes, possibly throughout the genome? Or attainment of a “new and original function”? In the latter case who judges newness and originality of function?

    JF is competely confused about ID and functional information here. I have only tried to explain, by the thief example, that complex information is always referred to one function, and that it is completely different from:

    “changes anywhere in the genome, as long as they contribute to the fitness”

    IOWs, complex functional information is the single safe with the complex key.

    “changes anywhere in the genome, as long as they contribute to the fitness” are the many safes with simple keys.

    If JF thinks that the 500 bits threshold stated by Dembski and used by me refers to the sum of many independent changes, he has understood nothing of ID theory.

  469. 469
    Antonin says:

    gpuccio:

    I would like to clairfy that I have never “tried to get someone to call Joe Felsenstein’s attention”. I have simply posted my old argument, specifying that it was a criticism to a statement by Joe Felsenstein, and that, as far as I am aware, he has never answered that particular point.

    Sure. It was my suggestion to pass on a head-up. I don’t know if mung or someone else did so or whether Professor Felsenstein independently noticed comments when preparing his article at The Panda’s Thumb.

    In all events, your scenario should now get an airing.

    My thoughts regarding your (shall-we-say) evolution-critical articles here at UD involving you performing number crunching on raw sequence data is that it doesn’t bear on reality. The difficulty is that you have spread your argument over several opening posts and many comments so it’s hard to know what your best and most concise exposition is. Not wanting to create work for you but how much effort would it take to cut and paste the salient points into an abstract or summary with links to the original material. Apologies if you already did this and I missed it. A downloadable PDF would be marvelous!

    You are far from a BA77 or a KF but a little editing, fact from opinion, would be helpful.

  470. 470
    Antonin says:

    JF is competely confused about ID and functional information here.

    Unconfuse him then! The problem seems to be that that definitions seem to vary depending on who is defining. JF at PT (after listing a number of critiques of Dembski’s various stances on CSI):

    So only Dembski’s first argument, the one using the Law of Conservation of Complex Specified Information, even tried to show that there was some information-based Law that prevented natural selection from putting adaptive information into the genome. And, as we’ve seen, that law does not work to do that. And Holloway seems to have missed that. As he missed all these other refutations of Dembski.

  471. 471
    EugeneS says:

    Eric:

    The standard definition of information (due to Shannon):

    https://en.wikipedia.org/wiki/Information_theory

    Natural processes CAN create information as per that definition. To deny that is wrong and makes various people think that ID is moot.

    BUT (and it is a big ‘but’)

    the amount of functional information (defined differently) that a natural process can generate is bounded in practice. It is just a fact of life evo supporters cannot come to terms with.

    Various notable figures in biological physics like Pattee have acknowledged at different times that information in Shannon’s sense is NOT suitable for a description of biological processes. The juggling magic tricks with Shannon’s information that folks like J Shallit are in favor of, miss the point entirely. An allusion to this is perhaps the C paradox.

  472. 472
    ET says:

    Earth to Antonin- There isn’t any “unconfusing him”. Joe F doesn’t want to understand ID. He relishes in erecting strawman after strawman and then knocking them down.

    Natural selection is impotent and so are all of Joe F’s arguments against ID.

  473. 473
    Mung says:

    EugeneS:

    The standard definition of information (due to Shannon)

    I have a lot of respect for you and I agree that ID supporters should be extra careful when talking about information, but I do not see a definition of information in that page. I see definition for various entropies.

    Surely there is a difference between information and entropy. If not why not?

    Thanks

  474. 474
    gpuccio says:

    Antonin:

    The idea of a pdf is not bad. Maybe I could work at it, let’s see.

    However, I cannot believe that, as EugeneS says, people, including JF, still have problems to understand the idea of specified information and functional information. It’s not so difficult.

    Anyone can understand that a machine, or a software, or a text, or a protein, needs a minimal level of bit complexity to do what it does. It’s such a simple and intuitive idea that it is a real mystery how people try to deny it.

    I have not yet read JF’s article about Dembski. As I am not a mathematician, I try not do discuss details of general theories about information, information conservation, and so on.

    As I have said many times, I have problems with the famous Dembski paper about specification. Maybe it’s just my limited mathematical proficiency.

    But the basci idea of specified information, and in particular of functionally specified information, is simple beautiful and universal. I have only tried ot express it in empirical terms that can easily be applied to biology.

    JF has explicitly criticized my arguments as if my idea that functional information must be computed for one explicitly defined function were some weird addition to ID theory. But that’s not true.

    All examples of functional information discussed in biological settings are of the kind. How can JF insist that many simple mutations that give reproductive advantage, happening “anywhere in the genome”, add up to generate 500 bits of functional information? What argument is this?

    Those are independent events, simple events, that can be naturally selected if the increase “fitness”, exactly as the thief can gain from different safes with simple keys.

    That has nothing to do with complex functional information.

    The alpha and beta chains of ATP synthase are complex functional information. A single object (indeed, just part of it) that requires hundreds of specific AAS to work. That’s the big safe. That’s what cannot be reached by RV + NS, because:

    a) RV cannot find anything that needs more than 500 bits of functional complexity to implement its function.

    b) There is no naturally selectable path to a complex function which cannot exist without at least 500 bits of information already there.

    The fact that complex proteins require a lot of specific information wo work is absolutely incontrovertible: even those biologists that are honest enough to recognize the importance of functional information admit it. See Szostak. Even JF admits that the concept of functional information is important, even if immediately after he demonstrates that he has not understood it at all.

    My application of a simple procedure to compute FI in proteins is really simple too. The idea is simple and powerful. We know there is FI in proteins. How can we approximate its value?

    The answer is: functional conservation of the sequence thoough long evolutionary times. It’s an answer directly derived from the only part of the neo-darwinist paradigm that works: the idea of negative NS, aka purifying selection.

    The idea is not mine, of course. It’s there in all biological thought. Durston was probably the first to apply it in a definite bioinformatic procedure. Mine idea is essentially the same, even if the procedure is somewhat different. As I have explained in detail many times.

  475. 475
    Mung says:

    gpuccio:

    Why don’t you just try to “point out the flaws” in my approach yourself?

    I would, but I couldn’t find any. 😀

  476. 476
    gpuccio says:

    Mung:

    Just a humble suggestion.

    Maybe we should avodi to use the word “information”, at least without further clarifications.

    So, if I say:

    The potential total information content of a sequence

    the concept is clear: it’s a^n, where a is the number of possible symbols, and n is the length. That is clear.

    If I say:

    The Kolmogorov complexity of a sequence

    that is well defined too, it’s the shortest “program” that can generate the sequence in some environment.

    If I say:

    The functional information of a sequence for function x, explicitly defined

    again, it’s clear: it’s the ratio between the target space of all sequences that imlement that function and the search space of all possible sequences (always in a well defined environment or system).

    But if I say:

    The information in this object or sequence

    What does it mean?

    It’s better to be precise, rather than looking for some universal definition of information that does not exist.

  477. 477
    Mung says:

    EricMH @ 464. Well said!

    Sadly, it’s a struggle to get some information theory experts to first cop to the fact that (Shannon) entropy measures the probability distribution.

  478. 478
    gpuccio says:

    Mung:

    “I would, but I couldn’t find any.”

    And, coming from you, that’s really flattering! 🙂

    Indeed, that request was made to Antonin. With you, I would probably be a little scared! 🙂

  479. 479
    gpuccio says:

    Mung:

    You say:

    “(Shannon) entropy measures the probability distribution”

    Please, accept a simple thought that comes from my long practice of statistics.

    I don’t think that we can “measure” a probability distribution. A probability distribution is a mathematical object. I think what you mean is that Shannon’s entropy uses a probability distribution to effect measures on empirical objects.

    Please, correct me if I am wrong about your thought.

  480. 480
    EricMH says:

    @EugeneS, check out the “entropy is not information” article by Dr. Schneider.

  481. 481
    Mung says:

    gpuccio:

    It’s better to be precise, rather than looking for some universal definition of information that does not exist.

    🙂

    I almost agree with what you have said in your post. A caveat. If we are talking about “Shannon information” then we should say entropy and not information unless we are talking about “mutual information.”

    Using the term “entropy” is absolutely defensible from the literature on information theory. Cover and Thomas is a classic text. They barely use the word information at all.

    Personally, after having read Arieh Ben-Name for years, I go one step further and try to avoid using the term entropy because that term has a specific meaning within thermodynamics and statistical mechanics and it is not the same as shannon entropy. People get confused.

    Shannon entropy has a far broader scope as it applies to any probability distribution. Thermodynamic entropy does not.

    So the alternative suggested by Ben-Naim is SMI. The Shannon Measure of Information. It’s idiosyncratic, but clearly delineates the subject matter.

  482. 482
    Mung says:

    kairosfocus:

    As for defining a probability, that is an exercise in itself in Mathematics and philosophy.

    🙂

    Worth the read:

    Probability Theory: The Logic of Science

    Kolmogorov developed an axiomatic approach to probability. I hear it works if you’re willing to accept the axioms.

  483. 483
    Mung says:

    gpuccio:

    I don’t think that we can “measure” a probability distribution. A probability distribution is a mathematical object. I think what you mean is that Shannon’s entropy uses a probability distribution to effect measures on empirical objects.

    How about if we think of a probability distribution as a potential model? It may or may not model an empirical object. We can plug numbers into it that have no relation to anything. It may be entirely abstract.

    As long as values are assigned for the probabilities we can “measure” the “information” associated with that distribution. There is no necessary connexion with anything material or empirical or any other object other than the mathematical object that is the distribution itself.

    That’s what I think.

  484. 484
    EugeneS says:

    Mung:

    Thanks for the correction. Here it is on Shannon information:

    https://en.wikipedia.org/wiki/Information

    This is how I understand the connection.

    The notions of information and entropy are closely related. For states with min entropy (e.g. at 0K), information that the observer gets when such a state is realized is minimum. At high temperatures, the information provided by observations increases (because states are getting towards equiprobable).

    It is not without a reason that information entropy H is measured in bits.

  485. 485
    EugeneS says:

    Eric, Thanks.

  486. 486
    Antonin says:

    The idea of a pdf is not bad. Maybe I could work at it, let’s see.

    Well, good!

    However, I cannot believe that, as EugeneS says, people, including JF, still have problems to understand the idea of specified information and functional information. It’s not so difficult.

    I don’t think that’s the problem. Joe Felsenstein’s complaint is that definitions, not least Dembski’s, have morphed. He’s asking ID proponents to decide on a definitive (heh) definition.

    Anyone can understand that a machine, or a software, or a text, or a protein, needs a minimal level of bit complexity to do what it does. It’s such a simple and intuitive idea that it is a real mystery how people try to deny it.

    But a protein is not a text, is not a machine, is not software. Analogies may help in understanding, they can also mislead.

    I have not yet read JF’s article about Dembski. As I am not a mathematician, I try not do discuss details of general theories about information, information conservation, and so on.

    One thing I’ve learned from following scientific arguments is that math is a powerful analytical tool and mathematical modelling has served science well. But it has also led some to revere the model rather than be sure how well it fits reality. Map and territory!

    As I have said many times, I have problems with the famous Dembski paper about specification. Maybe it’s just my limited mathematical proficiency.

    Felsenstein has issues there too. Dembski has changed his definition more than once.

    But the basci idea of specified information, and in particular of functionally specified information, is simple beautiful and universal. I have only tried ot express it in empirical terms that can easily be applied to biology.

    I think you fall into that trap I just mentioned. Doesn’t matter how elegant the model if it doesn’t tally with reality.

    JF has explicitly criticized my arguments as if my idea that functional information must be computed for one explicitly defined function were some weird addition to ID theory. But that’s not true.

    All examples of functional information discussed in biological settings are of the kind. How can JF insist that many simple mutations that give reproductive advantage, happening “anywhere in the genome”, add up to generate 500 bits of functional information? What argument is this?

    Those are independent events, simple events, that can be naturally selected if the increase “fitness”, exactly as the thief can gain from different safes with simple keys.

    That has nothing to do with complex functional information.

    I’m sure Professor Felsenstein will address your points but let me just repeat you seem to have a fundamental misconception about how evolution is postulated to work. And the assumption of “islands of function” is an assertion that doesn’t bear scrutiny.

    The alpha and beta chains of ATP synthase are complex functional information. A single object (indeed, just part of it) that requires hundreds of specific AAS to work. That’s the big safe. That’s what cannot be reached by RV + NS

    (I sense some Texas sharpshooting coming up)

    …because:

    a) RV cannot find anything that needs more than 500 bits of functional complexity to implement its function.

    But evolution is not a tornado in a junkyard. There can be intermediates. This arbitrary claim of 500 bits is just, well, arbitrary! 🙂

    b) There is no naturally selectable path to a complex function which cannot exist without at least 500 bits of information already there.

    See above

    The fact that complex proteins require a lot of specific information wo work is absolutely incontrovertible: even those biologists that are honest enough to recognize the importance of functional information admit it. See Szostak. Even JF admits that the concept of functional information is important, even if immediately after he demonstrates that he has not understood it at all.

    My application of a simple procedure to compute FI in proteins is really simple too. The idea is simple and powerful. We know there is FI in proteins. How can we approximate its value?

    The answer is: functional conservation of the sequence thoough long evolutionary times. It’s an answer directly derived from the only part of the neo-darwinist paradigm that works: the idea of negative NS, aka purifying selection.

    The idea is not mine, of course. It’s there in all biological thought. Durston was probably the first to apply it in a definite bioinformatic procedure. Mine idea is essentially the same, even if the procedure is somewhat different. As I have explained in detail many times.

    *Googles Durston* Ah, Dr Kirk Durston. I see he’s entered the lion’s den at The Skeptical Zone. He appears to make the same assumption (erroneous in my view and I’m far from alone) that function is rare in sequence space. You should compare notes.

  487. 487
    bill cole says:

    Eric Gpuccio Mung

    This was posted yesterday at TSZ.

    Eric Holloway needs our help (new post at Panda’s Thumb)
    Posted on November 7, 2018 by Joe Felsenstein
    14
    Just a note that I have put up a new post at Panda’s Thumb in response to a post by Eric Holloway at the Discovery Institute’s new blog Mind Matters. Holloway declares that critics have totally failed to refute William Dembski’s use of Complex Specified Information to diagnose Design. At PT, I argue in detail that this is an exactly backwards reading of the outcome of the argument.

    Commenters can post there, or here — I will try to keep track of both.

    There has been a discussion of Holloway’s argument by Holloway and others at Uncommon Descent as well (links in the PT post). gpuccio also comments there trying to get someone to call my attention to an argument about Complex Functional Information that gpuccio made in the discussion of that earlier. I will try to post a response on that here soon, separate from this thread.

  488. 488
    kairosfocus says:

    GP, 463, that’s why I termed them descriptively, loading enzymes. KF

  489. 489
    kairosfocus says:

    EMH,

    that’s a really weird twist! Entropy is informational, but it is not information (and for sure not functionally specific coded information), why Brillouin spoke of negentropy way back.

    Let me give the telling clip against interest from Wiki on entropy, again:

    At an everyday practical level the links between information entropy and thermodynamic entropy are not close. Physicists and chemists are apt to be more interested in changes in entropy as a system spontaneously evolves away from its initial conditions, in accordance with the second law of thermodynamics, rather than an unchanging probability distribution. And, as the numerical smallness of Boltzmann’s constant kB indicates, the changes in S / kB for even minute amounts of substances in chemical and physical processes represent amounts of entropy which are so large as to be right off the scale compared to anything seen in data compression or signal processing.

    But, at a multidisciplinary level, connections can be made between thermodynamic and informational entropy, although it took many years in the development of the theories of statistical mechanics and information theory to make the relationship fully apparent. In fact, in the view of Jaynes (1957), thermodynamics should be seen as an application of Shannon’s information theory: the thermodynamic entropy is interpreted as being an estimate of the amount of further Shannon information needed to define the detailed microscopic state of the system, that remains uncommunicated by a description solely in terms of the macroscopic variables of classical thermodynamics. For example, adding heat to a system increases its thermodynamic entropy because it increases the number of possible microscopic states that it could be in, thus making any complete state description longer. (See article: maximum entropy thermodynamics.[Also,another article remarks: >>in the words of G. N. Lewis writing about chemical entropy in 1930, Gain in entropy always means loss of information, and nothing more” . . . in the discrete case using base two logarithms, the reduced Gibbs entropy is equal to the minimum number of yes/no questions that need to be answered in order to fully specify the microstate, given that we know the macrostate.>>]) Maxwell’s demon can (hypothetically) reduce the thermodynamic entropy of a system by using information about the states of individual molecules; but, as Landauer (from 1961) and co-workers have shown, to function the demon himself must increase thermodynamic entropy in the process, by at least the amount of Shannon information he proposes to first acquire and store; and so the total entropy does not decrease (which resolves the paradox).

    Summarising Harry Robertson’s Statistical Thermophysics (Prentice-Hall International, 1993) — excerpting desperately and adding emphases and explanatory comments, we can see, perhaps, that this should not be so surprising after all. (In effect, since we do not possess detailed knowledge of the states of the vary large number of microscopic particles of thermal systems [typically ~ 10^20 to 10^26; a mole of substance containing ~ 6.023*10^23 particles; i.e. the Avogadro Number], we can only view them in terms of those gross averages we term thermodynamic variables [pressure, temperature, etc], and so we cannot take advantage of knowledge of such individual particle states that would give us a richer harvest of work, etc.)

    For, as he astutely observes on pp. vii – viii:

    . . . the standard assertion that molecular chaos exists is nothing more than a poorly disguised admission of ignorance, or lack of detailed information about the dynamic state of a system . . . . If I am able to perceive order, I may be able to use it to extract work from the system, but if I am unaware of internal correlations, I cannot use them for macroscopic dynamical purposes. On this basis, I shall distinguish heat from work, and thermal energy from other forms . . .

    Observe again, from Gilbert Newton Lewis as echoed by Wikipedia:

    in the words of G. N. Lewis writing about chemical entropy in 1930, Gain in entropy always means loss of information, and nothing more” . . . in the discrete case using base two logarithms, the reduced Gibbs entropy is equal to the minimum number of yes/no questions that need to be answered in order to fully specify the microstate, given that we know the macrostate.

    Anyone so confused as to imagine the opposite is missing the heart of the matter.

    KF

  490. 490
    EricMH says:

    @bill cole, thanks. I think Felsenstein misunderstood what I am saying.

    > I was struck by Bill Dembski’s claim that ID could be demonstrated mathematically through information theory.

    I am merely pointing out that Dembski’s claims that CSI cannot be generated by natural processes is supported by information theory.

    Whether biological entities have CSI or not is a separate matter. Perhaps they do, perhaps they don’t. But at any rate, the theoretical framework of Dembski’s is valid, and if CSI is detected then it indicates intelligent design. I am currently looking into FI and other approaches to see if any qualify as the right sort of algorithmic mutual information. The “unreasonable effectiveness of mathematics in the natural sciences” strikes me in particular as mutual information with an independent variable, since mathematics is not produced by the physical world.

    https://www.dartmouth.edu/~matc/MathDrama/reading/Wigner.html

    Also, I saw that you only found Levin’s Russian publication. Here is his English paper that talks about conservation of information in section 1.2.

    https://core.ac.uk/download/pdf/82092683.pdf

    I have a high level explanation how halting oracles make an empirical difference:

    https://www.am-nat.org/site/halting-oracles-as-intelligent-agents/

    and a mathematically detailed overview of Levin’s proof, and how a halting oracle can violate his law:

    https://www.am-nat.org/site/law-of-information-non-growth/

  491. 491
    ET says:

    Antonin:

    But a protein is not a text, is not a machine, is not software.

    They exist and their existence is due to a code and the components required to carry it out in the required manner. So to that end they need to be explained.

    But evolution is not a tornado in a junkyard.

    This is not about mere evolution. This is about evolution by means of blind and mindless processes

    There can be intermediates. This arbitrary claim of 500 bits is just, well, arbitrary!

    Yes, it is arbitrary and way too high. There isn’t any evidence for blind and mindless processes coming close to that figure. Dembski used it only because it allegedly breaches the upper probability bound.

    He appears to make the same assumption (erroneous in my view and I’m far from alone) that function is rare in sequence space.

    Where is the peer-review or any science to support YOUR claim? Can YOU or anyone else show that function is abundant, or whatever your claim is, in sequence space?

    By the way starting with living organisms means you are starting with the very things that need explaining. And that is all you, Joe F or anyone else can do.

  492. 492
    kairosfocus says:

    PS: Observe from Wiki’s admissions, how entropy is informational (noting that in effect we can always round a continuous to a discrete quantity):

    in the discrete case using base two logarithms, the reduced Gibbs entropy is equal to the minimum number of yes/no questions that need to be answered in order to fully specify the microstate, given that we know the macrostate.

    In short, entropy is an index of missing info to get the microstate, starting from the macro.

    PPS: I should add, that the 500 – 1,000 bit complexity threshold as reasonable upper limits for sol system or observed cosmos can readily be understood. Consider the 10^57 atoms of our sol system as observers; each updating observations of a tray of 500 coins every 10^-12 to 10^-15s. Run this exercise for 10^17 s, let’s use -14. We have a grand total of 10^(57 + 17 + 14) = 10^88 possible observations. 2^500 possible states of 500 coins = 3.27*10^150. In short, a yardstick for negligible possible blind search of a config space. The 1000 bit version is even more generous for the solar system. Too much haystack, too little time and resources to search blindly hoping to come across a needle.

  493. 493
    Antonin says:

    This is about evolution by means of blind and mindless processes

    Exactly! The model is not the reality! Thanks for confirming that. I might even revise my opinion of you as an interlocutor! 🙂

  494. 494
    Antonin says:

    KF:

    In short, entropy is an index of missing info to get the microstate, starting from the macro.

    Careful with that, though. It leads to the idea that entropy is in the mind of the observer. Better informed observers, reduction in entropy. Completely informed observer – zero entropy. Can that be right?

  495. 495
    ET says:

    Felsenstein is clueless:

    Starting in 2005, Dembski changed the definition of his CSI. He’d say that he clarified it, showing what he had meant all along. But after 2005, his original LCCSI is no longer discussed. Instead he has a new way of proving that CSI cannot be achieved by natural evolutionary forces: he simply refuses to define the population as having CSI if its state can be achieved by natural evolutionary forces! It’s only CSI if evolution can’t get there. So how do we know that? He doesn’t say — it’s up to us to find a way to show that, in order to be able to call it CSI. Which reverses the whole effect of showing something has CSI. CSI formerly was being used to show evolution couldn’t get there. Now we have to separately show (somehow) that evolution can’t get there before we can call it CSI. Which makes CSI a useless add-on to the whole argument. Dembski’s new argument will be found here. It was published in Philosophia Christi in 2005. Some further comments on the new argument by me will be found here (comments are missing as in many older PT threads — we hope to restore them some day soon).

    Wrong!

    In 2005 Wm Dembski revised/ refined his views on “specification” and he never said anything about a population cannot have CSI if it arose via blind and mindless processes. That is total BS by Felsenstein.

    CSI exists regardless of how it came to be. The point is materialistic processes cannot produce it. No one even knows how to go about demonstrating such a thing.

    Then Joe F mumbles something about fitness when that really isn’t even the issue. Increased fitness can occur with a loss of functionality.

    We can easily dismantle Shallit and Elsberry, too

  496. 496
    kairosfocus says:

    F/N: configurationally specific, complex function will be exceedingly rare and isolated in a space of possible configs i/l/o that threshold, as say shaking a bait bucket full of 6500 fishing reel parts and hoping to assemble the reel will illustrate. Do not let dismissive rhetoric against a Nobel equivalent prize holder mislead you into thinking the problem is not real. Ponder the search challenge to find functional strings of 500 bits as just shown, to see what is being said. If you don’t like coins, ponder a paramagnetic substance in a weak aligning field as a more obviously physical case. And — notice how confusions and dismissals compound — the D/RNA string for a 300 AA protein will be about 900 bases long, each base having 4 possible states. That is, 1800 bits of raw information storing capacity. The codes used and the synonyms etc plus the patterns of what varies and what does not for a given protein across the world of life will reduce info content but not anywhere near enough to undermine the Fermi calc for a cell with 500 proteins. OoL by blind chance and/or mechanical necessity is a non-starter, never mind hopeful scenarios. More to the point, we find a coherent code with algorithms reflecting a deep knowledge base of AA sequence possibilities, and associated with a complex molecular tech cybernetic system. The evidence is clear enough that blind mechanisms are utterly implausible explanations for the world of life from its root. KF

  497. 497
    ET says:

    Antonin:

    The model is not the reality!

    That’s your opinion. You don’t seem to be able to support anything that you post, though.

    And the fact that you couldn’t see that Felsenstein is blowing smoke proves that you don’t deserve to be in a discussion here.

  498. 498
    kairosfocus says:

    Antonin, is info stored in a hard drive in the mind of an observer? If the drive were wiped with a random pattern, would that be anywhere likely to ever be functional, regardless of how many times it were done within sol system scale resources? Why or why not? KF

  499. 499
    ET says:

    More cluelessness from Felsenstein:

    If we have a population of DNA sequences, we can imagine a case with four alleles of equal frequency. At a particular position in the DNA, one allele has A, one has C, one has G, and one has T. There is complete uncertainty about the sequence at this position. Now suppose that C has 10% higher fitness than A, G, or T (which have equal fitnesses). The usual equations of population genetics will predict the rise of the frequency of the C allele. After 84 generations, 99.9001% of the copies of the gene will have the C allele.

    This is an increase of information: the fourfold uncertainty about the allele has been replaced by near-certainty. It is also specified information — the population has more and more individuals of high fitness, so that the distribution of alleles in the population moves further and further into the upper tail of the original distribution of fitnesses.

    Unbelievable. The sad part is he really thinks that he has something there. The “information” in CSI pertains to a sequence or sequences, either nucleotides or amino acids that perform specific functions, with respect to biology. It also pertains to individuals within a population.

  500. 500
    gpuccio says:

    Mung:

    “I almost agree with what you have said in your post. A caveat. If we are talking about “Shannon information” then we should say entropy and not information unless we are talking about “mutual information.””

    I am very fine with that! 🙂

    “How about if we think of a probability distribution as a potential model? It may or may not model an empirical object. We can plug numbers into it that have no relation to anything. It may be entirely abstract.”

    I think we essentially agree, except a little in terminology.

    A probability distribution is a mathematical object. It becomes a model when we use it to model some data.

    Now, those data (the numbers we try to model by the mathematical object) are usually derived from real empirical scenarios. Or they can, of course, be arbitrary: in that case, it would be a simulation of modeling.

    However, there is a subtle difference between the distribution, which is a mathematical object, and the model realized using that distribution. For example, the model has residues, and so on, because usually the distribution does not fit perfectly the data.

    The normal distribution is an invariable mathematical object. When we apply it to model real data, we have specific values for mean, standard deviation and so on.

    That said, I think we agree.

  501. 501
    EricMH says:

    @Bob O’H, I missed a comment of yours:

    > EricMH @ 272 – if ASC is a hypothesis test w.r.t. a specific hypothesis, then you should be able to provide the maths to show how you go from the hypothesis to ASC as a test statistic. I can see how you can do that for CSI (because of the relationship between Shannon’s entropy and the multinomial distribution), but not ASC.

    The specific hypothesis would be addressed by the probability distribution used to measure self information. Same idea as with the complexity term in CSI. I may be still misunderstanding you.

  502. 502
    gpuccio says:

    Antonin:

    I don’t think that’s the problem. Joe Felsenstein’s complaint is that definitions, not least Dembski’s, have morphed. He’s asking ID proponents to decide on a definitive (heh) definition.

    Funtional information is a true concept. It works, It is there. Definitions can change, but the concept remains true.

    I am rather sure that my definition works, so I stick to it.

    As I always say, ID is not a political party. We are here, all of us, to understand what is true. Including JF.

    But a protein is not a text, is not a machine, is not software. Analogies may help in understanding, they can also mislead.

    Wrong. A protein is certainly not a text, and it is somewhat different from a software. But it is definitely a machine. Or at least, most of them.

    This is not an analogy. It is a simple and obvious truth.

    One thing I’ve learned from following scientific arguments is that math is a powerful analytical tool and mathematical modelling has served science well. But it has also led some to revere the model rather than be sure how well it fits reality. Map and territory!

    Of course. I am a big fan of the map and territory idea. Got it from my limited frequentations with NLP.

    Felsenstein has issues there too. Dembski has changed his definition more than once.

    Maybe. However, I haven’t.

    Note: I am not saying in any way that I am any better than Dembski. Just stating that I have been sticking to my definition, probably for lack of creative thought! 🙂

    I think you fall into that trap I just mentioned. Doesn’t matter how elegant the model if it doesn’t tally with reality.

    It’s you that are falling into a trap, in particular a bad analogy, or rather a good analogy badly used.

    Of course no model corresponds to reality. But there are good models and bad models, and science is about choosing among different models.

    Going back to the map and territory issue, you certainly understand that a map is a good map if it is useful for what we have to do.

    Complex functional information is a very good map to infer design, and that is exactly what we want to do.

    I have never said that any map corresponds to reality, even ID theory. But a good map is useful to understand reality better.

    More in next post.

  503. 503
    gpuccio says:

    Antonin:

    I’m sure Professor Felsenstein will address your points but let me just repeat you seem to have a fundamental misconception about how evolution is postulated to work. And the assumption of “islands of function” is an assertion that doesn’t bear scrutiny.

    What misconception? Details, please.

    Why doesn’t it bear scrutiny? I have given reasons for my “assumption”. You haven’t given any against it.

    More in next post.

  504. 504
    EricMH says:

    @Bill Cole and Joe Felsenstein: here’s an analogy for what I see with information theory and ID. In quantum physics there is something known as Bell’s theorem which has been used to disprove local realism. Bell derived from first principles a distribution that quantum experiments must follow if local realism is true. All experiments have shown that quantum experiments do not follow the distribution. Thus we know local realism is false.

    In a similar manner, Levin’s law gives a distribution that all physical phenomena must follow of it is purely the result of Turing reducible processes and random oracles (natural causes). Thus, if what we actually observe does not follow the distribution, then we can eliminate what I am labeling “natural causes” as a complete explanation for the natural world.

    Levin’s law also seems to let us go further and identify a distribution generated by “halting oracles,” potentially giving us the ability to make positive identification of halting oracles in our universe.

    https://www.am-nat.org/site/halting-oracles-as-intelligent-agents/

    https://www.am-nat.org/site/law-of-information-non-growth/

    This is equivalent to what Dembski’s work shows. Hence my claim that Dembski’s argument is supported by information theory.

  505. 505
    kairosfocus says:

    F/N: For convenience, Wiki:

    The macroscopic state of a system is characterized by a distribution on the microstates. The entropy of this distribution is given by the Gibbs entropy formula, named after J. Willard Gibbs. For a classical system (i.e., a collection of classical particles) with a discrete set of microstates, if E i {\displaystyle E_{i}} E_{i} is the energy of microstate i, and p i {\displaystyle p_{i}} p_{i} is the probability that it occurs during the system’s fluctuations, then the entropy of the system is

    S = ? k B [SUM on i] p i ln p i

    Entropy changes for systems in a canonical state

    A system with a well-defined temperature, i.e., one in thermal equilibrium with a thermal reservoir, has a probability of being in a microstate i given by Boltzmann’s distribution.

    The quantity k B {\displaystyle k_{\text{B}}} k_{\text{B}} is a physical constant known as Boltzmann’s constant, which, like the entropy, has units of heat capacity. The logarithm is dimensionless.

    This definition remains meaningful even when the system is far away from equilibrium. Other definitions assume that the system is in thermal equilibrium, either as an isolated system, or as a system in exchange with its surroundings. The set of microstates (with probability distribution) on which the sum is done is called a statistical ensemble. Each type of statistical ensemble (micro-canonical, canonical, grand-canonical, etc.) describes a different configuration of the system’s exchanges with the outside, varying from a completely isolated system to a system that can exchange one or more quantities with a reservoir, like energy, volume or molecules. In every ensemble, the equilibrium configuration of the system is dictated by the maximization of the entropy of the union of the system and its reservoir, according to the second law of thermodynamics (see the statistical mechanics article).

    Neglecting correlations (or, more generally, statistical dependencies) between the states of individual particles will lead to an incorrect probability distribution on the microstates and thence to an overestimate of the entropy.[1] Such correlations occur in any system with nontrivially interacting particles, that is, in all systems more complex than an ideal gas.

    This S is almost universally called simply the entropy. It can also be called the statistical entropy or the thermodynamic entropy without changing the meaning. Note the above expression of the statistical entropy is a discretized version of Shannon entropy. The von Neumann entropy formula is an extension of the Gibbs entropy formula to the quantum mechanical case.

    KF

  506. 506
    kairosfocus says:

    S = – k_B [SUM on i] p_i ln p_i

    This brings in distribution of Pi across possible microstates i

  507. 507

    Antonin at #453

    What I suspect you are objecting to is the evolvability of the current process from simpler precursors.

    I simply laid out a well-recorded history of thought on the subject. Pierce modeled the physical capacity to specify something among alternatives; requiring a representation, a referent, and a separate interpretant to establish what was being represented. This model is dead center of any materialist view of the physical cosmos. Turing built that same triadic relationship into his 1936 machine — indeed; it was the entire mechanism behind the machine’s ability to function. Von Neumann then used that machine to successfully predict the material requirements of an autonomous self-replicator. His predictions were wholly confirmed by Crick’s discovery of a reading frame code in DNA and his further prediction that a set of Piercean constraints would be found at work in the system. These were later isolated by Hoagland and Zamecnik, while Nirenberg et al went on to list the individual associations established by the constraints. And all of this has since been carefully and meticulously described in the physics literature as the only other example of a general purpose (sequential, multi-referent) language (other than human language) found anywhere in the cosmos. This also includes the additional organizational requirement of being semantically closed in order to function (i.e. to persist over time). You might ask yourself why you viewed the listing of these historical facts as an attack on “evolutionary theory”.

    We can only surmise what the biochemistry was like in the earliest organisms that could both grow and replicate.

    Well, okay. I imagine we can do a bit more than that. We can follow established scientific reasoning and infer that the forces and substances in nature acted (back then) just as they do today. Likewise, we can infer that any theory that requires those forces and substances to act differently (back then) than they do today (accomplishing effects they’ve never been known or recorded to accomplish) are less grounded in evidence and reason than theories that do not require such things — in particular, theories that expect nature to have acted (back then) exactly as it does today, and proposes causes that are known (and well-documented) to be adequate to explain the phenomena.

    My question to you is ‘what is it’ empirically-speaking that motivates the idea that the gene system isn’t exactly what it was predicted to be (a semantically-closed, sequential, multi-referent symbol system, using a medium of information established by a set of physical constraints) confirmed by experiment and fully described by physics?

    Alternatively, we can certainly assume that some form of biologically-relevant constituents came together at a common place on earth. We can further assume that these constituents all came together in the necessary quantities in some form of conducive environment. We can then assume that some unknown sequential dynamic replicator formed in that environment.

    We can further assume that while this dynamic replicator replicated, it also dynamically produced some form of discrete product that could serve as a constraint to establish a first unique informational relationship. We can further assume that while this sequence kept on replicating it produced a second discrete product to serve as a constraint. We can then assume, one by one, more discrete products were produced by the dynamics of this unknown sequence. We can go on to assume that along its length, it continued replicating dynamically as it produced all the constraints necessary to describe itself in a symbol system, along with all the additional products that would cause it to bring its symbols and constraints together in a hierarchy capable of transitioning from a dynamic replicator to a symbolic replicator. Or we can shuffle all those things around and come up with a whole new set of assumptions. Likewise, we can simply ignore the logic that any organization which must maintain its function as it transitions from one system of description to another must (at some point in that transition) function in both systems. We can also ignore how many constraints are required to synthesize a constraint from memory. And we can certainly ignore the simultaneous organization required for semantic closure to occur.

    Is this the bottom line for you? Do you believe that, given the documented physical evidence (with its genuine history of prediction and discovery), there is simply no room for dispute about the validity of materialists’ assumptions — that is, there is no intellectual or scientifically-respectable dissent from materialism? Is this not where you are at? Or, or do you have a positioning statement to retain the line in practice while seeming otherwise?

  508. 508
    gpuccio says:

    Antonin:

    *Googles Durston* Ah, Dr Kirk Durston. I see he’s entered the lion’s den at The Skeptical Zone. He appears to make the same assumption (erroneous in my view and I’m far from alone) that function is rare in sequence space. You should compare notes.

    We have probably similar ideas.

  509. 509
    gpuccio says:

    Antonin:

    From:

    “Your approach is not persuasive”

    to:

    “Good grief!”

    to:

    “Just, well, arbitrary!”

    it’s a remarkable escalation! 🙂

  510. 510
    kairosfocus says:

    Antonin, it is not an assumption that configuration based function will be rare in sequence space or in configuration space in general, especially code oriented function. First, it is a readily confirmed observation that it is exceedingly difficult to obtain long enough coded strings by blind processes where by contrast unconstrained variation will as a rule produce non-functional gibberish. Likewise, in wider config spaces (which on description languages are reducible to strings, see AutoCAD etc), requisites of functional configuration generally require assembly in accord with a wiring diagram of some type, implicit or explicit. This is contrasted with something as loose as scattered or clumped in any order, which leads straight to very large spaces indeed. The example of a 6500 fishing reel is a simple, direct illustration, as is the million monkeys type simulation exercise. So, in effect you are defying abundant observation and are putting up “assumption” as a case of selectively hyperskeptical dismissal. Your observed evidence for complex code-functional configurations being common in sequence spaces and for similar any clumped or scattered order wiring patterns having functionality that is not rare in the space of possibilities is: ________ . Complex here is measured by requiring at least 500 – 1,000 bits of information to describe in a reasonably compact description language. KF

  511. 511

    Ah, forgot to mention … thanks to all for the kind words upthread.

  512. 512
    Nonlin.org says:

    gpuccio @440,

    Meanwhile, YOU were the one forced to agree with me. Does that tell you anything? It should.

    Yes, logic becomes unbearable when you find yourself in a corner.

  513. 513
    Nonlin.org says:

    kairosfocus @442, 443

    Not sure what your point is. You talk about “weighted average information per symbol”, but know that information is not tied to specific symbols. Example: you can represent a ‘circle’ in English or any other language, as math equation, descriptive, etc. Each one of those employs different symbols.

    Somehow I have the feeling we’re talking past each other again.

    From your site:
    “One of these, is that when we see regularities of nature, we are seeing low contingency, reliably observable, spontaneous patterns and therefore scientifically explain such by law-like mechanical necessity: e.g. an unsupported heavy object, reliably, falls by “force of gravity.” But, where we see instead high contingency — e.g., which side of a die will be uppermost when it falls — this is chance [“accident”] or intent [“design”]. Then, if we further notice that the observed highly contingent pattern is otherwise very highly improbable [i.e. “complex”] and is independently functionally specified, it is most credible that it is so by design, not accident. ”

    Do you understand where we differ on this passage?

  514. 514
    Mung says:

    Upright BiPed:

    Ah, forgot to mention … thanks to all for the kind words upthread.

    If I spoke any kind words I can assure you it was not sincere.

  515. 515
    Mung says:

    gpuccio:

    What misconception?

    That you can reason with someone who cannot be reasoned with.

  516. 516
    Mung says:

    EricMH:

    The specific hypothesis would be addressed by the probability distribution used to measure self information.

    I think this language is imprecise. There is no probability distribution that measures self-information. Self-information is mutual information. There is no probability distribution that measures mutual information.

    I’m still working out how to put this all in plain language so forgive me for stopping here. 🙂

    self-information

  517. 517
  518. 518
    EricMH says:

    @Mung, too many terms! In this case I have a precise meaning. ASC has a ‘self information’ quantity which is the -log of the probability for X according to some chance hypothesis. Maybe I’ll call this quantity “point SMI” since it deals with a particular instance instead of the whole distribution, while per your usage SMI refers to the whole distribution.

    Separate topic, can anyone reduce FI to simple terms and math to save me having to read gpuccio’s links? I know the basic idea that it is the difference of two SMIs, but what are the underlying distributions the SMIs are measuring, why are they subtracted, and why is FI rare? If no one wants to, that is fine. I will get around to gpuccio’s links sooner or later.

    And thanks everyone, this has been an illuminating thread!

  519. 519
    EricMH says:

    @ET regarding Felsenstein’s example, this sounds the same as Dawkin’s weasel program. Why does he not find the standard response by Marks and Ewert convincing, that the CSI is just being propagated by the fitness function, so no creating of CSI is taking place? I keep getting the impression the skeptics are not trying to understand the argument.

  520. 520
    bill cole says:

    Eric

    and why is FI rare?

    Depends on the function how rare it is. There appears to be a range. Gpuccio measures “rareness” by amino acid preservation over time. This demonstrates that high sequence specificity was required.

    gpuccio can describe his method in more detail. There are many highly preserved proteins gpuccio has identified.

  521. 521
    gpuccio says:

    EricMH:

    “Separate topic, can anyone reduce FI to simple terms and math to save me having to read gpuccio’s links? I know the basic idea that it is the difference of two SMIs, but what are the underlying distributions the SMIs are measuring, why are they subtracted, and why is FI rare? If no one wants to, that is fine. I will get around to gpuccio’s links sooner or later.”

    well, I can try, even if I am not sure that I understand correctly your questions. So, I will try, and you can clarify if necessary.

    FI is the probability of the emergence of one object in the target set in a well defined material system, without any design intervention, by the probabilistic resources of the system itself.

    I think this is in perfect accord with Dembski’s original ideas (IOWs, the explanatory system).

    The target set is defined in relation to one explicitly defined function. Any function definition can be used, provided that it is explicit and that it specifies an explicit way to test any object in the system to asses if it can implement the function or not. IOWs, we must have an objective procedure to assess, at least in principle, for any possible object in the system if the function is present or not.

    Of course, any measure of FI is related to its explicitly defined function.

    In most systems, and certainly in most biological systems, we can assume an uniform probability distribution in the system, where the probability fo each object to emerge is approximately the same.

    Of course, that is not literally true, but as I will try to explain it is the best approximation for our purposes.

    With that assumption, the probability of the emergence of one object in the target set (IOWs, the FI for that target set defined by the function) is simply the negative of the ratio between the target space and the search space (IOWs between the two numerosities).

    If we express the two numerosities in base 2, we just take -log2 as the value of FI in bits.

    Let’s take the case of one protein, or class of proteins, with a well defined function.

    A forst assumption, to make the computations possible, is to assume a reference length for tha protein, which can be derived form the existing functional protein or proteins.

    In Durston’s terms, we compute the search space simply as the value in base 2 of 20^n (where n is the reference length). That is rather simple.

    The problem is in computing the numerosisty of the target space. There is no problem in principle: for each possible protein sequence there is a way to verify if the function is present or not, as defined in the function definition. But of course, for any length that is not trivial, that is, and always will be, empirically impossible.

    So, we need indirect methods. As our uinderstanding of the sequence-function relationship in proteins is limited, we cannot just derive the result from a coomputation. Not yet.

    So, we can use protein conservation.

    Durston uses one approach, I use a slightly different one.

    Durston aligns a number of existing sequences in that protein family, from different species, and then computes the Shannon entropy in that set, defined by the common function.

    I use human protein sequences as a “probe” to evaluate human conserved information in distant groups of organisms, using the BLAST tool, that eveluates the level of homology between sequences.

    There are pros and cons in both methods, but in the end they measure the same thing, conserved information, and I believe that the results are reasonably similar.

    I will explain here in more detail, but very briefly, my approach.

    The basic assumption is that sequence conservation through long evolutionary times is a good measure of functional constraint.

    That is in perfect accord with the neo-darwinist model, and there are many empirical confirmations for this idea. I will not go into biological details here, but we can discuss the reasons for that if you are interested.

    In my analyses, I have usually considered the transition to vertebrtaes as a good object of study. The reson for thatis that:

    a) It is very interesting.

    b) It took place more than 400 million years ago, which is enough to make my meausres of human conserved information a reliable indicator of functional constraint.

    OK, I wil say something more about the assumtpion of an uniform probability distribution in next post.

  522. 522
    kairosfocus says:

    Nonlin, symbols implies a communication context where distinct symbols in context convey meaningful or functional messages. ASCII-based alphanumeric text strings in English, as in this thread, is an example of this in action. Similarly, D/RNA has meaningful coded symbols used to assemble proteins step by step, again not controversial. If you will go to my Sec A in my always linked you will see an outline of how we get to Shannon Entropy, which is indeed the weighted average info per symbol. This is fairly standard stuff dating to Shannon’s work in 1948. The similarity to the Gibbs expression for entropy created much interest and as I noted Jaynes et al have developed an informational perspective on thermodynamics that makes sense of it. Thermodynamic entropy is effectively an index of missing info to specify microstate for a system in a given macrostate. For, there are many ways for particles, momentum/energy etc to be arranged consistent with a macrostate. As for the clip from my online note, I an simply speaking to the longstanding trichotomy of law of mechanical necessity vs blind chance contingency on closely similar initial conditions, vs functionally specific complex organisation and associated information. While we can have an onward discussion of how laws and circumstances of the world are designed [per fine tuning] or that randomness can be used as part of a design, the issue here is to discern on empirically grounded reliable sign, whether the more or less IMMEDIATE cause of an effect is intelligently directed configuration or is plausibly explained on blind chance and/or mechanical necessity. KF

  523. 523
    kairosfocus says:

    sorry, missing information.

  524. 524
  525. 525
    gpuccio says:

    EricMH:

    About the probability distribution.

    Of course, we must always consider the physical system we are analyzing.

    So, let’s talk proteins.

    In the biological system, where the main source of unguided variation is random point mutations, the true nature of the random system is a random wlalk rather than a random search (while a random search model is still valid for certain types of variation, like frameshift mutations).

    However, that is no real problem, provided we clarify what we are doing.

    Of course, in a random walk in the sequence space, sequences that are nearer to the starting point have higher probabilities to be reached. Indeed, with one single point mutation event, only sequences that differ of 1 AA from the starting point can be reached.

    But we can easily overcome that problem by defining the terms of our analysis. What we are interested in, from an ID point of view, is the emergence of a new complex function from an unrelated sequence. IOWs, we are interested to a transition that involves more than 500 bits of FI.

    For example, the 2000 protein superfamilies are completely unrelated both at sequence level and at function level (indeed, even at structure level).

    So, when a new protein superfamily emerges in natural history, it is a real novelty both at sequence level and at function level.

    And, of course, we must allow for a high number of events to explain the transition. We can allow up to the probabilistic resource of the biological system, that I have computed to be (very generously!), at most, 138.6 bits (2^138.6 events). See here, Table 1:

    What are the limits of Random Variation? A simple evaluation of the probabilistic resources of our biological world

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-random-variation-a-simple-evaluation-of-the-probabilistic-resources-of-our-biological-world/

    So, with a high number of events, any sequence in the search space can certainly be reached. Of course, we are not considering here possible effects of NS. Let’s say that our model starts with a non coding non functional sequence, so that the effectf of NS are avoided, at least until a selectable function emerges.

    Now, we can reason this way. There is a certain number of states in the search space that are obviously more likely: indeed, all the states that are significantly related at sequence level with the starting sequence.

    So, we can ideally divide the search space into two subsets:

    a) States which are more or less related to the starting sequence, at sequence level.

    b) States that are completely unrelated to the starting sequence at sequence level (let’s say that they show no significant homology with it).

    Now, subset a) is certanly hugely smaller than subset b), for sequences that are not trivially long. We also know that our target space is somewher in sibset b), because we are considering the emergence of a new sequence, unrelated to what already existed. A new protein superfamily.

    So, for the moment, let’s ignore subset a).

    My simple point is that all the states in subset b) can be considered approximately equiprobable in a random walk starting form the unrelated sequence.

    Even if we consider the effect of subset a), it can only lower the average probability of sequences in subset b), because of course sequences in subset a) are more likely to be reached by a random walk.

    So, considering the probability of each state in the search space as 1/n is a good approximation, indeed a slight overestimation for the probability of unrelated states (and therefore of the target space).

    Of course, the probabilities of individual sequences can be slighlty different, for example according to their AA composition. The genetic code is not symmetric, some AAs are more likely than others in point mutations, and some mutations are more likely than others. And there are certainly other biochemical factors that can generate non uniformity in the probability of the individual states.

    But that’s not really important, because of course none of those “anomalies” can explain or favour specific functional sequences. And even if they could slightly favour one of them, then they would not favour the others, because, as we know, functional sequences at the superfamily level are sequence unrelated. They have different sequences, different AA composition, and so on.

    So, for all practical purposes, assuming an uniform distribution in the search space is the best approximation.

    One final point: my analysis is not limited to protein superfamilies. It is valid for all complex transitions. When I apply my procedure based on homologies and conservation through long evolutionary times, I am always interested in what I call an “information jump”.

    IOWs, I don’t consider the absolute conserved information in a protein, but the difference (jump) in human conserved information between two evolutionary nodes: usually, between pre-vertebrates and vertebrates.

    That is a “jump”: it means that I am cosnidering the emergence of a new sequence, even if it is part of an older protein, that already exhibited some human conserved homology.

    I hope that’s clear. Of course I am available to clarify any point, if necessary.

  526. 526
    gpuccio says:

    EricMH:

    One more point.

    FI is “rare” only when it is related to a complex function.

    FI related to simple functions is not rare at all.

    That’s why simple functions (involving a transition of 1 or 2 AAs, like in antibiotic resistance) can easily emerge in a biological system from RV.

    But complex functions are extremely rare, and isolated.

  527. 527
    EugeneS says:

    GP

    “But complex functions are extremely rare, and isolated.”

    This one is very important. It came up a few times in my own discussions with biologists, who claimed guess what?… that once we have a minimal functioning organism it can achieve all the rest 🙂

  528. 528
    EricMH says:

    @gpuccio, thanks a lot. Very clear. I think the uniform hypothesis was my big question. You are right, that the Kullback-Liebler divergence between the uniform distribution and your specification is going to always be smaller than between some arbitrary distribution and your specification, so the uniform minimizes the FI score. Also, the KLD with the uniform simplifies to H(U) – H(P), so I see where Durston gets his formula.

    Here’s a Python simulation to demonstrate the point:

    https://repl.it/@EricHolloway/KLD-for-FI

    gives the result:

    kld(u,p): 0.43
    kld(u,q): 0.44
    kld(p,q): 0.73
    kld(u,p)<kld(p,q): True
    kld(u,q)<kld(p,q): True

    Here’s a follow on question. How can we apply this method to another domain, say photography or text? Assuming the uniform distribution seems like it’ll always give me a very high FI score. Maybe that is because the FI is actually very high.

    Also, is there a way to identify new FI? Examples: identifying an out of place object in a photograph, plagiarism in text, an intrusion in a network, a virus on the computer, steganography in spam, or spies in a population.

  529. 529
    gpuccio says:

    EugeneS:

    “This one is very important. It came up a few times in my own discussions with biologists, who claimed guess what?… that once we have a minimal functioning organism it can achieve all the rest”

    Why am I not surprised? 🙂

  530. 530
    Antonin says:

    @ gpuccio, KF and Upright Biped

    I may have time over the weekend to respond to outstanding comments but I’m in a bit of a quandary whether to continue here. I don’t mind abuse when it’s directed at me but I’m more than a little disappointed with the discussion on another thread. It should be obvious at a glance what I’m referring to. If not… Well, that says something in itself, no?

  531. 531
    Antonin says:

    …complex functions are extremely rare, and isolated…

    And so much else to pick up on! 🙂

  532. 532
    gpuccio says:

    EricMH:

    Very interesting example, thank you.

    And very good questions. Let’s see.

    a) Photography. This is interesting.

    Of course, a camera is certainly a designed object with a lot of FI.

    But let’s say that the camera is already part of our system. So, we have a photo, and we want to know if the photo itself is a designed object.

    Let’s say that the photo represents, with good fidelity, a room (furniture, etc).

    The question is: can we infer design for the object “photo” in our system?

    My answer is no.

    There can be no doubt that the photo seems to exhibit a lot of FI: the function can easily be defined in terms of representing well enough what it represents (see later the discussion about text for more details). And certainly, the target space/search space ratio will be extremely small, and the potential FI extremely high. There should be no problems in iferring design…

    But… there is, indeed, a proble. The problem is necessity.

    Because our system includes a tool, the camera, that can easily shoot that photo, even without a design intervention from a conscious being (like pushing the shooting button, which however would be a very simple design intervention). For example, however weird it can seem, some material object falling on the button for random reasons could well shoot the photo.

    This is very interesting, and demonstrates how important it is to include the system in our analysis. If the system already includes some mechanism of necessity that could in principle generate the complex object, maybe as the consequence of some random, but not completely unlikely, event, then design is not necessarily the explanation for the object.

    To be more clear:

    a) In our system, the camera is certainly designed: I cannot imagine any explanation for tha camera that does not include a lot of design intervention to produce the camera, with the specification of many, many bits of functional information to get the working configuration.

    b) Given the camera, the photo of the room does not add any big amount of FI. OK, the act of pushing the button requires usually a simple design intervention, but the FI in it is very low. The point is that the wonderful ability of the photo to represent the room derives directly from the optical properties of the light coming from the room itself, even if thorugh the compex action of the camera. IOWs, given the camera, it is the light itself, thorugh physical laws of necessity, that generates the photo and its informational content. So, given the camera, necessity is here the good explanation, and not design, for the complex configuration of the photo.

    That is often true for information that directly derives, analogically, from a form already existing in the system.

    Now, let’s say instead that we have not a photo, but a good drawing of the room, made with coloured pencils by a good designer. Here, the reasoning is different, because the nature of the object in our system can easily exclude any necessity origin. IOWs, there is no natural law that converts thorugh light the form of the room into a drawing (if we can exclude that our system includes some complex science fiction machinery designed to draw by coloured pencil).

    The meaning of all that is that we must be very careful to exclude possible necessity mechanisms that can explain the configuration that we are observing.

    However, in the absence of a designed camera, I don’t think that it is easy to find a system that could generating something similar to a photo just from the natural pattern of light in the environment. But I cannot exclude it, because in a way that information is potentially already there, in the reflected light.

    More in next post.

  533. 533
    kairosfocus says:

    ES, a minimally functioning single cell organism is a molecular nanotech based, encapsulated, smart gated automaton that has metabolic systems coupled to code controlled fabricators and a von Neumann kinematic self replicator. “Simple” is exactly what such is not! KF

  534. 534
    gpuccio says:

    Antonin:

    “It should be obvious at a glance what I’m referring to.”

    I don’t know if it’s obvious. I have not looked much at other threads, while I was busy here. Can you specify better?

  535. 535
    gpuccio says:

    EricMH:

    Let’s go to text.

    That is easier, because text is digital and symbolic. That helps.

    However, both images and text are usually examples of descriptive information, not prescriptive information. They convey meanings, rather than implement a function (which is the purpose of prescriptive information).

    While it is always possible to convert descriptive information into a functional form to measure it, that is often tricky.

    For example, we can define the function of an image or a text as being able to convey to an observer some specific and well defined meaning, but of course it is not completely obvious how to do that. The comprehension of a text can be difficult to measure objectively, for example. And the same is true for images.

    This is an objection that is often exploited by neo-darwinists (or in general critics of ID): where is the threshold to say that the cloud is really like a weasel, and not a camel or a whale? Or to conclude, correctly, that it is only a cloud with some simple and contingent resemblance to other things?

    For FI proper (prescriptive information) it’s much easier to define a function and a way to evaluate it.

    However, some indirect method for FI in a text can be more easily applied. For example, in my OP:

    An attempt at computing dFSCI for English language

    https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/

    I have used a simple approach and a minimal functional definition to compute a lower threshold for FI in a Shakepseare sonnet. With good results, IMO. So, it is possible.

    You ask:

    “Also, is there a way to identify new FI?”

    Of course. That’s exactly what I do when I analyze information jumps in the transition to vertebrates.

    “Examples: identifying an out of place object in a photograph”

    Of course, it is easy to identify an out of place object in a photograph, if you have the reference photograph. The problem is: is that variation complex and functiona? I can imagine many scenario where that is not true, and other where it could be true.

    Again, it is important to consider the system, and to define a function to measure the FI.

    “plagiarism in text,”

    That should not be difficult, if we have references. And of course, a plagiarim that is well adapted to the context would be functional and, if complex enought, an indicator of design, while a simple occurrence of some parapgraph out of context could be a random event.

    “an intrusion in a network, a virus on the computer, steganography in spam, or spies in a population.”

    Again detection is not necessarily difficult. I think that machine learning can deal with some of those scenarios quite efficiently. The problem always remains to find some way of defining a function to measure FI. Again, it’s not impossible, but it can be tricky.

    In the end, the purpose is always to detect a conscious intervention that has assembled specific bits of information to generate an extremely unlikely configuration defined by a complex function.

  536. 536
    EricMH says:

    @gpuccio, how about computer code then, since that is prescriptive? We can use the repl.it I posted, since it is not trivial, but also not very long.

    https://repl.it/@EricHolloway/KLD-for-FI

    How would we measure the baseline, and how would we measure function?

    My naive approach is to measure baseline by len(code)*log(len(alphabet),2).

    Function is a bit more difficult. I think it is a proportion of how many character strings of that length result in compilable code. It would be intractable to approach in a bruteforce manner, but clearly most such character strings are broken code, so the functional measure would be very small. I think it could be tractably upper bounded by all the lexeme variations that can fit in the string length.

    Thus, I’d lower bound FI for computer code with:
    len(code)*log(len(alphabet),2) – log(number of lexeme variations, 2) = very big number.

    Is my understanding of how to apply FI correct here, gpuccio?

    Also, do you have a link to your work:

    > That’s exactly what I do when I analyze information jumps in the transition to vertebrates.

    Being able to detect new FI seems very useful. For example, say we have a code generation tool. Obviously, it comes with background FI. How can we determine if a code base is only generated by the tool vs a code base written from scratch? This would be detected by a significant amount of new FI compared to the code generation tool baseline.

  537. 537
    gpuccio says:

    EricMH:

    Again, very good questions! This converstation is really interesting. 🙂

    First of all, the link to ifnormation jump OPs. Indeed, there are a number of them.

    This one:

    Homologies, differences and information jumps

    is probably mi first explicit application of the procedure, applied tp a very interesting regulatory protein, Prickle 1.

    https://uncommondescent.com/intelligent-design/homologies-differences-and-information-jumps/

    In the second one:

    The highly engineered transition to vertebrates: an example of functional information analysis

    https://uncommondescent.com/intelligent-design/the-highly-engineered-transition-to-vertebrates-an-example-of-functional-information-analysis/

    I apply the ame procedure to a small group of proteins.

    In the third one:

    The amazing level of engineering in the transition to the vertebrate proteome: a global analysis

    https://uncommondescent.com/intelligent-design/the-amazing-level-of-engineering-in-the-transition-to-the-vertebrate-proteome-a-global-analysis/

    I have done the “big work”: I have applied the procedure to the whole human genome, 20000 proteins, using it as a probe against the main gorups of organisms in Metazoa. The results are very, very interesting.

    You are perfectly right: computer code is prescriptive information, and it sollows the same rules as proteins and protein genes: they are all examples of digital prescriptive information.

    Yes, your procedure is perfectly correct. That’s the idea.

    As you say, with sequences of some length it’s impossible to test the function directly, “in a bruteforce manner”, as you say. We have to use indirect methods.

    The same is true for proteins.

    In the case of some simple algorithm, the procedure would be:

    a) We observe a program that is functional in a certain context, for example a sorting algorithm.

    b) We define explicitly the function (taking lists of words as input and sorting them in alphabetical ascending order as output). We can also define a measure for the existence of the function, for example being able to sort a reference list of 1000 words. We can also set a threshold of efficiency (in less than 1 msec). The important thing is that everything is explicit and not ambiguous, so that anyone can apply our definition and procedure to an object (in this case, a sequence of bits in the computer) and verify if that sequence works as a program that can implement the function.

    c) We compute the search space. You are correct, this is the easy part, and your procedure is perfectly correct. Just a few comments about the problem of length.

    The simplest way to act is what you have described: we take the length of the reference object (the program we are analyzing for FI) and use that length to define the search space.

    With computer programs, in order to minimize the search space, it would be fine to use as reference the shortest program available that can do the job. Even if we can never be sure that one program is the shortest, empirically it’s perfectly fine to work with what is known and available. That will set a reasonable minimum size of the search space. The existence of possible longer programs that are functional should not be a problem, because in general FI increases with the length of the functional sequence, and we want to find the minimun FI linked to our defined function.

    d) As you say, the size of the target space is the real difficult step. We have to use all possible strategies to get reasonable approximations.

    In the case of computer programs, I believe that the target space is usually rather small. IOWs, computer programs should not be very tolerant to bit substitutions. I am not an expert, but it seems reasonable. So, the FI will always be very high if the search space is big enough (that is usually the case even with simple computer programs).

    Indeed, I cannot think of any complete and independent computer program, however simple, that is so functionally simple that it can be easily found by a random search. Correct me if I am wrong. Of course, it is probably possible to get, by a random search, some simple set of instructions that can be functional in the appropriate context. IOWs, a functional sequence with low FI.

    For proteins things are rather different, because we know that protein sequences are certainly more tolerant to AA substituions than computer programs are to bit substitutions. How much they are tolerant is key to measure their target space, and indeed that is still a very open problem, one that is often used by neo-darwinists to unleash their imagination, assuming extremely huge functional spaces with wonderful functional connections. All things never observed, of course, because very simply they do not exist.

    The simple truth is that the functional space of proteins obeys similar rules as the functional space of computer programs: simple functions can abound, but complex functions are rare and isolated in the sequence space.

    We know that: we know that all functional proteins that we have observed have been classified into 2000 superfamilies of sequences, all of them unrelated at the level of sequence, structure and function. Unlike darwinists, we have no need to imagine the functional islands: they are there, in front of us.

    However, as said, it is true that those functional islands, even if rare and isolated, are bigger for proteins than they are for computer programs.

    Just an example that I often use.

    The alpha and beta chains of ATP synthase are a very good example of highly conserved sequences. In this case, I am not evaluating an information jump in vertebrates, but just the total conserved sequence information between E. coli, a bacterium, and humans. About 2 billion years of separation, reasonably.

    Well, as said at #148 here, the homology between the two sequences (E. coli andhuman), evaluated by BLAST, is as follows:

    alpha chain = 561 bits

    beta chain = 663 bits

    total = 1224 bits

    As I have said, there are good reasons to believe that BLAST gives a severe underestimation of the real FI, but let’s take it as it is.

    1224 bits of FI for these two chains, that are functionally one thing because together they make the main part of the F1 subunit of the protein.

    OK, but what is the search space?

    Using our procedure, we can see that the search space for both protein is as follows:

    alpha chain: length = 553 AAs

    beta chain: length = 529 AAs

    total length = 1082 AAs

    So, as a gross evaluation, the search space is about 20^1082, that is about 4676 bits.

    Our estimated FI is about 1224 bits.

    What does that means? It means that we are estimating a target space of:

    4676 – 1224 = 3452 bits!

    IOWs, a target space of 2^3452 sequences.

    That is certainly an overestimation, but again let’s take it as true.

    So (for those who are not familiar with that kind of computation, not you of course), we have:

    2^3452 (target space) / 2^4676 (search space) = 2^-1224

    FI = -log2(2^-1224) = 1224 bits

    I don’t believe that the true target space is so big, but I accept the results of the BLAST algorithm, even if they certainly underestimate severely FI, because it is a reliable and easy to use tool to evaluate homologies, universally used. And it’s fime with me to underestimate FI and give neo-darwinists some “help”. I can be satisfied with 1224 bits of FI for one biological object! 🙂

    So, we can see that even huge target spaces are rare and isolated islands of function in the ocean of the sequence space.

    More in next post.

  538. 538
    gpuccio says:

    EricMH::

    Finally, you say:

    “Being able to detect new FI seems very useful. For example, say we have a code generation tool. Obviously, it comes with background FI. How can we determine if a code base is only generated by the tool vs a code base written from scratch? This would be detected by a significant amount of new FI compared to the code generation tool baseline.”

    Being able to detect new FI is certainly very useful, and not difficult.

    For example, in the case of Prickle 1 in my first linked OP, the second part of the protein, the blue part in my OP, suddenly acquires about 600 bits of sequence information that did not exist in pre-vertebrates and that are then fully conserved up to humans, for more than 400 million years. Those 600 bits are a novelty, and a novelty that appears in about 30 million years (the reasonable time span of the transition to vertebrates).

    Moreover, they are 600 bits of functional information: otherwise, how can we explain that they have been conserved for 400+ million years of exposure to neutral variation?

    So, we can detect new FI in proteins. And it is indeed very useful.

    Let’s see if I understand well your interesting scenario of the code generation tool.

    You say:

    You say:

    “Obviously, it comes with background FI.”

    That’s absolutely true: it’s the FI linked to the function of the tool: generating codes. It can reasonably be computed or estimated.

    You say:

    “How can we determine if a code base is only generated by the tool vs a code base written from scratch? This would be detected by a significant amount of new FI compared to the code generation tool baseline.”

    Again, perfectly true. A couple of interesting thoughts.

    a) The tool can probably generate codes that are apparently more complex than the tool otself, in terms of length and apparent FI. That can be done by using the computational abilities programmed in the tool itself.

    We are here in the same situation as described about programs that compute the digits of pi. At some point, the apparent functional complexity of the output will be greater that the functional complexity of the generating program.

    But that is really not true: the generating program is indeed a valid compression of the output, so the Kolmogorov complexity of the output, if its apparent functional complexity is greater than the functional complexity of the tool, is by definition the functional complexity of the tool itself. IOWs, the functional complexity of the tool is a higher threshold for the functional complexity of the output.

    IOWs, a merely computing tool cannot generate FI significantly higher than the FI it already has. (I have added “significantly” because, as we know, low levels of FI can be added incorporating RV in the algorithm).

    What about programs that use RV + Artificial selection? We know they can achieve good results, in terms of FI. Not so good as a system that includes new design interventions, but good results just the same. We have good demonstration of that in the procedures of protein engineering, that are often rather successful in optimizing proteins, sometimes even in generating some gross new ones.

    What is the limit here?

    The limits are two:

    1) These are the limited but important powers of Artificial selection. They must not be confused with the extremely limited powers of Natural selection. I have discussed the differences here:

    Natural Selection vs Artificial Selection

    https://uncommondescent.com/intelligent-design/natural-selection-vs-artificial-selection/

    2) Artificial selection as implemented by a non conscious tool, however good, can only optimize a function that has already been defined and programmed in the tool. Directly or indirectly. Nothing else.

    Again, the FI in the tool is the real limit of what the tool can do.

    Only conscious, intelligent and purposeful agents can think, define and recognize new and original functions. That power comes from their conscious experiences and representations, as I have briefly discussed at #465 here.

    So, this is not a mathematical law of conservation, but just a very simple and empirical truth:

    Machines can only do what they have been programmed to do.

    They can use RV if they have been programmed to do that, but only in the way they have been programmed to do.

    They can use RV + AS if they have been programmed to do that, but only in the way they have been programmed to do, and for the function they have been programmed to select for.

    They can incorporate new information form the outside world, or from their inner simulations, but only in the way they have been programmed to do.

    Very simply, they can compute about already defined functions, because their FI has been designed to do exactly that.

    But they can never create, recognize or implement new, original functions.

    Why?

    Because they are not conscious. They do not understand any meaning. They have no desires. For those who, like me, believe in free will, they have no free will.

    So, a new functional specification, which cannot be derived from the existing FI or computed from it, and that is complex enough, is an extremely reliable indicator of conscious design.

  539. 539
    EricMH says:

    @Bill Cole, Joe Felsenstein, and Tom English,

    With a bit more time on my hands, I took a look at Dr. Felsenstein’s claim that Dembski’s law of conservation of information (LCCSI) is false:

    https://pandasthumb.org/archives/2018/11/Eric-Holloway-needs-our-help.html

    This is Dembski’s most important claim, because it proves natural processes cannot generate CSI. I reread Shallit & co.’s 2011 paper:

    http://web.cecs.pdx.edu/~mperk.....EMBSKI.pdf

    and to pick out what seems their clearest objection against LCCSI, on pg. 256 they say:

    To cover this possibility Dembski introduces the universal composition function U, defined by U(i, f ) = f (i) = j. He then argues that the amount of CSI in the pair (i, f ) is at least as much as j. Of course, this claim also suffers from the two problems mentioned above, but now there is yet another error: Dembski does not discuss how to determine the CSI contained in f.

    First of all, Dembski is correct. Since K(x, U(x)) = K(x), we can show

    I(x:y) > I(U(x):y),

    which is the same as showing

    I(f,i:j) > I(U(f.i):j).

    This is straightforward algorithmic information theory, so it is unclear why a professor of computer science is taking issue with Dembski’s claim here.

    Second, they call a lack of discussion an ‘error.’ That is a novel use of the term ‘error,’ and by that definition there are many relevant pieces of information Shallit does not discuss in his paper, so he makes a multitude of errors as well. Seems like an unhelpful definition of error, and certainly not a usage that shows Dembski’s theory is false. It raises the question in my mind, if Shallit says Dembski’s theory is in error, does he mean it is false or does he mean Dembski hasn’t covered something that Shallit is interested in?

    Back to Felsenstein’s original post, he says the problem with Dembski’s argument is the target must be independent, and this is covered when Dembski says the specification must be detachable.

    So, from my brief perusal of Felsenstein’s response, I’ll have to say that Felsenstein has repeated the pattern I continue to detect, that the skeptics are saying straightforward information theory is highly controversial merely because it shows up in Dembski’s argumentation. Otherwise, they just don’t read Dembski’s work very carefully.

  540. 540
    bill cole says:

    Hi Eric

    So, from my brief perusal of Felsenstein’s response, I’ll have to say that Felsenstein has repeated the pattern I continue to detect, that the skeptics are saying straightforward information theory is highly controversial merely because it shows up in Dembski’s argumentation. Otherwise, they just don’t read Dembski’s work very carefully.

    Although I am getting comfortable with you proof I need to spend more time with it. I really like your collaboration with gpuccio as I have tremendous respect for him. I think Demski is right and believe the objections by Tom and Joe are just the best they can do trying to refute a solid claim.

    Question: Would you consider a AA sequence for the same protein in humans as in chimps where there are slight variation as mutual information?

  541. 541
    EricMH says:

    @bill cole, while shared proteins is a form of mutual information, it is not the sort that is required for my argument. The target Y has to be independent from the formation of X. A better example is the effectiveness of mathematics for describing the natural world. Mathematics is an independent target because the physical world did not create mathematics.

  542. 542
    EricMH says:

    This line is incorrect in my response to Felsenstein:

    I(f,i:j) > I(U(f.i):j)

    should be

    I(f,i:y) > I(U(f.i):y).

    U is a universal Turing machine applied to the concatenation of f and i, which is the same as executing function f on input i.

  543. 543
    bill cole says:

    Hi Eric
    I just read part of Shallit’s argument and his first two main points are philosophical. I have to give credit to Joshua for engaging you technically as he is the only one that is doing this. I don’t find his argument as a credible challenge but he is engaging on a technical level.

  544. 544
    EricMH says:

    Thanks Bill, that is encouraging 🙂 I am happy to be disproven, but as you say it needs to be on a technical level.

  545. 545
    Mung says:

    EricMH:

    Also, I saw that you only found Levin’s Russian publication. Here is his English paper that talks about conservation of information in section 1.2.

    Levin, L.A. Appears on nine pages in the book Information and Randomness

    I’ll have to check them out.

  546. 546
    Mung says:

    EricMH:

    ASC has a ‘self information’ quantity which is the -log of the probability for X according to some chance hypothesis.

    ASC is Algorithmic Specified Complexity?

    Is ASC based on Algorithmic Information Theory, which in turn is based on Kolmogorov Complexity?

    Chaitin identifies AIT1, AIT2, and AIT3. Of AIT1 he says it “is only of historical or pedagogic interest.”

  547. 547
    EricMH says:

    @Mung not sure about the AIT1-3 designation. ASC uses prefix-free Kolmogorov complexity for the specification term. The nice thing about prefix-free Kolmogorov complexity is it follows the Kraft inequality,

    sum 2^-K(x) < 1,

    so we can prove the probability ASC is >= a is <= 2^-a. Thus, high ASC is good evidence the chance hypothesis is false.

  548. 548
    Nonlin.org says:

    kairosfocus @522

    Sorry, you keep doing your monologue. I already explained, but let me know if you have any questions or counterarguments to my comments.

  549. 549
    EricMH says:

    @gpuccio, thanks for your very in depth responses. I will be analyzing everything you wrote see if FI is addressed by Levin’s information conservation.

  550. 550
    gpuccio says:

    EricMH:

    Thank you! I will be happy to know your thoughts. 🙂

  551. 551
    kairosfocus says:

    Nonlin, with all due respect, that is a rhetorically evasive dismissive one-liner in response to a substantial discussion. KF

    PS: For reference, 22, in response to an earlier bit of dismissiveness:

    >>symbols implies a communication context where distinct symbols in context convey meaningful or functional messages. ASCII-based alphanumeric text strings in English, as in this thread, is an example of this in action. Similarly, D/RNA has meaningful coded symbols used to assemble proteins step by step, again not controversial. If you will go to my Sec A in my always linked you will see an outline of how we get to Shannon Entropy, which is indeed the weighted average info per symbol. This is fairly standard stuff dating to Shannon’s work in 1948. The similarity to the Gibbs expression for entropy created much interest and as I noted Jaynes et al have developed an informational perspective on thermodynamics that makes sense of it. Thermodynamic entropy is effectively an index of missing info to specify microstate for a system in a given macrostate. For, there are many ways for particles, momentum/energy etc to be arranged consistent with a macrostate. As for the clip from my online note, I an simply speaking to the longstanding trichotomy of law of mechanical necessity vs blind chance contingency on closely similar initial conditions, vs functionally specific complex organisation and associated information. While we can have an onward discussion of how laws and circumstances of the world are designed [per fine tuning] or that randomness can be used as part of a design, the issue here is to discern on empirically grounded reliable sign, whether the more or less IMMEDIATE cause of an effect is intelligently directed configuration or is plausibly explained on blind chance and/or mechanical necessity.>>

  552. 552
    EugeneS says:

    KF 533,

    I have no problem with that, as you may already know 🙂

    Rather, what I am saying is that some of those biologists I converse with are ready to accept that intelligence was necessary to achieve that. However, they claim that, given this complex starting point, everything else is automatically achievable in the Darwinian manner.

  553. 553
    EricMH says:

    @ES, even with a complex starting point, Darwinian evolution is limited in how much variety it can produce. See this proof I published with Dr. Marks:

    Observation of Unbounded Novelty in Evolutionary Algorithms is Unknowable

    https://robertmarks.org/REPRINTS/2018_Observation-of-Unbounded-Novelty.pdf

    Open ended evolution seeks computational structures whereby creation of unbounded diversity and novelty are possible. However, research has run into a problem known as the “novelty plateau” where further creation of novelty is not observed. Using standard algorithmic information theory and Chaitin’s Incompleteness Theorem, we prove no algorithm can detect unlimited novelty. Therefore observation of unbounded novelty in computer evolutionary programs is nonalgorithmic and, in this sense, unknowable.

  554. 554
    EugeneS says:

    Eric,

    Of course. RV+NS can produce very low quantities of functional information, noise really.

    Thanks for the reference!

  555. 555
    EricMH says:

    @ES, well I wouldn’t say it “produces” the FI. Rather, the FI exists in the range of possibilities covered by RV+NS. If you take the expectation of ASC it is always non positive.

  556. 556
    EricMH says:

    Continuing the trend of the skeptics agreeing with ID whenever they speak in their domain of expertise, here is Dr. Tom English over at TSZ:

    http://theskepticalzone.com/wp.....ent-236757

    > The crucial point is that there are more ways for a discrete, deterministic universe to go than there are algorithms (finite sequences over a finite set of symbols) to describe how it goes.

    This is exactly the point that Jonathan Bartlett argues in the latest Blyth Institute book on alternatives to methodological naturalism.

    Another interesting point Dr. English makes:

    > I’m not aware of any biologist having claimed that evolution creates “new information” (whatever that is) out of nothing.

    So, again, this is what ID and Levin’s law of information non growth argue, and what Dr. Marks and I recently proved. Looks like Dr. English is on the same page with ID, at least in the formal theory he writes if not in his allegiances.

    Now, if he wants to call our theories “naturalism”, that’s fine by me. The empirical and theoretical formalisms are what matter, not the terms that Dr. English wants to use. If it’ll make Dr. English happy, we can call our theory the naturalistic theory of ID, with a natural soul and a natural creator of everything, and the natural teleological guidance of evolution and/or the natural special creation of creatures. We can all believe in a natural Christianity, founded by the natural Jesus who is both natural man and natural God.

  557. 557
    EricMH says:

    Regarding BruceS’ question about how the conservation of information applies to evolution if the environment is included in the evolution term:

    1. Since I(E,X:Y) >= I(U(E,X):Y), then evolution does nothing to explain the mutual information.

    2. Including the environment does not necessarily improve things. If K(K(E)|E) ~ 0, then including the environment is helpful. On the other hand, K(K(E)|E) ~ log K(E), then including the environment in evolution does not help increase the mutual information, so the original form,

    I(X:Y) >= I(U(E,X):Y),

    is still valid.

  558. 558
    EugeneS says:

    Eric,

    “Rather, the FI exists in the range of possibilities covered by RV+NS.”

    It is down to interpretation. If there is a local optimum within the reach of RV+NS of a given system, it can be found by random walk. If this is what you mean, we are talking about the same thing.

  559. 559
    ET says:

    Two points, guys:

    1- The first step of NS is RV-

    The first step in selection, the production of genetic variation, is almost exclusively a chance phenomenon except that the nature of the changes at a given locus is strongly constrained.- Ernst Mayr “What Evolution Is” page 281

    And it has to be heritable variation. “RV + NS” is redundant, like PIN number; ATM machine; DOA on arrival

    2- Unless there is pre-biotic natural selection- which has been called a contradiction in terms- when NS is discussed it is always in the presence of existing CSI/ FSCI/O.

  560. 560
    gpuccio says:

    ET:

    “Unless there is pre-biotic natural selection- which has been called a contradiction in terms- when NS is discussed it is always in the presence of existing CSI/ FSCI/O.”

    Of course.

    NS is indeed a very limited process that “recycles” in slightly different forms the FI already existing in the reproducing organism.

    It appears to be an adaptive optimization of some aspects in some cases, but in reality it is only a variation of the general balance of some given functional program, that already existed, given maybe a few bits of information variation in the environment.

    So, bacteria can change in a limited repertoire that expresses in different modalities the same FI that already was in the bacterium. They can lose a little bit of information in a molecule to become resistant to an antibiotic in the environment, they can change their ability to control citrate metabolism under strong environmental stress, they can use some existing molecule to digest nylon instead of penicillin when nylon becomes suddenly abundant.

    All those “optimizations” are simply random variations in the global expression of a huge program with huge FI that essentially defines that specific organism as a specific form of living organism, an already existing designed program which goes on implementing its original function: to make the organism’s life possible and to make the organism survive and reproduce.

    Probably, the global FI in that organism does not really increase, even if there are very small local increases for locally defined functions, always in the range of those few bits that are allowed by the essential limits of the probabilistic resource involved in biologic RV.

    The true jumps in FI that we observe so often in natural history are instead always examples of new plans involving new functional configurations that change deeply and in a coordinated way the whole plan of the existing organisms, adding new proteins or deeply re-engineered proteins, new control networks, new structures, and so on, IOWs a completely different perspective that can only be implemented controlling hundreds, thousands and even millions of functional bits in the process (see for example the transition to vertebrates, involving about 1.7 millions of functional bits).

  561. 561
    EricMH says:

    Another statement at odds with information theory over at TSZ:

    http://theskepticalzone.com/wp.....ent-237134

    > Conservation of information might make sense in terms of algorithmic information theory. But it makes no sense if we are talking about Shannon information, where we can generate as much new information as we want just because we decide to communicate.

    In Shannon information there is the data processing inequality, which says mutual information is conserved for markov chain X -> Y -> Z such that I(X;Y) >= I(X;Z).

    It is easy to convert this to Dembski’s CSI setting. If we set X to the specification and Y to the chance hypothesis, then per detachability P(Z|Y,X) = P(Z|Y), which is the markov property, and thus the DPI applies to CSI.

    Again, I do not understand why information theory experts do not see the connections between Dembski’s theory and well established information theory identities. It seems they are not trying very hard to understand Dembski’s work in the best possible light.

  562. 562
    EricMH says:

    At any rate, this latest exchange has confirmed my almost a decade old observation that the skeptics either agree with ID claims, or miss the obvious connections with information theory, even though they are “information theory experts.” The supposed controversy regarding Dembski’s theory of intelligent design is without merit. His claims are entirely consistent with well established information theory.

  563. 563
    bill cole says:

    Hi Eric

    At any rate, this latest exchange has confirmed my almost a decade old observation that the skeptics either agree with ID claims, or miss the obvious connections with information theory, even though they are “information theory experts.” The supposed controversy regarding Dembski’s theory of intelligent design is without merit. His claims are entirely consistent with well established information theory.

    I agree that all I see is hand waving. To a man all the objections are based on politics.

  564. 564
    EricMH says:

    For those interested in how Wigner’s unreasonable effectiveness of math in the natural sciences is a form of mutual information, the basic idea is straightforward. Say U is the universe and M is mathematics. The mutual information is I(U:M) = K(U) – K(U|M).

    Since the universe can be described mathematically, that means math allows us to compress the universe, so K(U) > K(U|M). Thus, I(U:M) > 0, and there is mutual information between the universe and mathematics.

    Furthermore, since mathematics exists independently from the universe, it is an independent target, and Levin’s law of information non-growth applies. If our explanation of the universe is restricted to naturalism, i.e. randomness and a universal Turing machine, then the expected mutual information between the universe and mathematics is 0.

    Therefore, since I(U:M) > 0, some other explanation, such as a halting oracle, is a better explanation for our universe.

  565. 565
    Mung says:

    EricMH:

    The mutual information is I(U:M) = K(U) – K(U|M).

    This is algorithmic mutual information?

  566. 566
    EricMH says:

    @Mung, yes algorithmic mutual information.

  567. 567
    EricMH says:

    @Mung, Bill Cole and Joe Felsenstein, My Wigner argument is basically an elaboration on Levin’s argument in his paper I keep referencing. For a more accessible overview of what Levin proved, see this Quora comment:

    https://www.quora.com/Will-mathematics-be-%E2%80%9Ccompleted%E2%80%9D-at-some-point-Will-there-be-a-time-when-there-is-nothing-more-to-add-to-the-body-of-mathematics-and-research-has-exhausted/answer/Claude-Taillefer?ch=10&share=13cbea14&srid=hW60T

  568. 568
    EricMH says:

    @Mung as Tom English pointed out I should have used the newer format for AMI:

    I(U:M) = K(U) – K(U|M*).

    The M* is the shortest program that outputs M, and makes the bound have only a constant error. The previous form I used has a logarithmic error.

  569. 569
    Mung says:

    thanks for the updates.

  570. 570
    EricMH says:

    We have a discussion going on over at TSZ on this topic:
    http://theskepticalzone.com/wp.....on-growth/

  571. 571
    ET says:

    Good luck with that. Neil already refuses to understand your point about intelligent agencies and halting oracles.

  572. 572
    jawa says:

    Perhaps what leading edge biology research is discovering these days can’t be understood using the currently available mathematical tools and scientific ideas. A superior way of abstract thinking might be required. The mind-boggling functional complexity we are observing demands a more serious approach to revising our current way of looking at it. This is a real scientific problem that requires honesty, humility and open mindedness. Too much talk won’t lead us anywhere worth being in. Let’s wake up and smell the flowers. Then get back to work. Biology has become the new queen of science, having math, physics, chemistry and other fundamental science fields as servants.
    Tomorrow will be more fascinating than today. Let’s just look ahead.

  573. 573
    EricMH says:

    @ET, BruceS has some excellent comments, and Tom English occasionally does as well. The rest is to be expected, but is still a step up from the passive aggressive appeals to authority at Peaceful Science.

    @Jawa, indeed, we need to totally revamp our scientific paradigm to make way for ID.

  574. 574
    ET says:

    Tom English is good at math but very bad at debating and understanding what is being debated. I don’t know Bruce but I will take your word for it. It looks like you have at least two people that will debate you without reverting to insulting you.

    That is a start and a good start at that.

  575. 575
    EricMH says:

    @ET agreed with Tom English. His latest OP on the “non conservation of ASC” is a good example of this. Excellent mathematical derivatives, but the entire article is based on misunderstanding ASC. However, the derivatives are useful, so I’ll give him that.

  576. 576
    EricMH says:

    Such purposeful obtuseness on the part of Neil Rickert and Tom English also shows the ID arguments have hit home. To keep making the point of the original article, I’ve noticed this trend ever since I started looking into ID over a decade ago.

    A slightly new approach is the peaceful pity party:

    https://discourse.peacefulscience.org/t/intelligence-as-a-halting-oracle/3063

  577. 577
    ET says:

    Eric, Neil thinks that a computer system’s OS is a blind and mindless process. He will do his best to not understand anything people who oppose hos personal point of view has to say

  578. 578
    ET says:

    Joe Felsenstein is still so clueless that he thinks if an allele rises to prominence in a given population then it is an increase of information because the uncertainty has been diminished. He has been told many times that this is wrong and yet he refuses to change.

    You cannot reason with people who are like that.

  579. 579
    EricMH says:

    Yes, it is a strange avoidance, because Marks and Ewert wrote an entire book on this exact scenario, along with numerous papers. Don’t know what to say, except it is a consistent pattern with the ID critics. Does that indicate intelligent design on their part? 😀

  580. 580
    ET says:

    Just look at this exchange between Bill Cole and Joe F:

    Bill: I think Eric’s argument is around the forming of the Genes themselves.

    Joe F: If so, it’s irrelevant to CSI.

    Not according to “No Free Lunch”. It is the sequence specificity that produces biological function that is the issue

  581. 581
    EricMH says:

    I put in my response to Tom English’s article. It has good math, but what it shows does not seem controversial to me. I’m holding off on the Wigner article because I want to have a good explanation for BruceS, and that’ll take a little time to put together.

  582. 582
    Mung says:

    EricMH:

    A slightly new approach is the peaceful pity party:

    Quite the contrast. Is that what people mean by an echo chamber?

    Joshua is big on finding points of agreement, but I’m not sure that extends to agreeing on anything when it comes to ID unless it’s that ID is bad.

  583. 583
    ET says:

    Joshua is also big on forming his own definition of “evolution”. If you disagree with universal common descent you are anti-evolution, which is weird because evolution isn’t defined that way.

  584. 584
    EricMH says:

    @Mung & ET, yes, Dr. Swamidass originally told me he’d be a step above the normal ID critic, but I just see more of the same, except now pretending to give ID a fair hearing. I prefer the normal critic that makes no such pretense, hence my foray over at TSZ.

    ‘Peace, peace,’ they say, when there is no peace. – Jeremiah

    I found TSZ to be fruitful from Dr. English and BruceS responses. Dr. Felsenstein also gave a simple scenario for me to illustrate the information conservation, so that was good too. I plan to head back when I have more relevant content to discuss.

  585. 585
    EricMH says:

    Something I would like to see over at PS is Dr. Swamidass defend his Adam and Eve idea. He spends a lot of time “ruthlessly destroying” other people’s theories, so for a change of pace it’d be interesting to see him articulate his own theory. It sounds pretty groundbreaking if Dr. Swamidass can show the proposed minimum bottleneck of 12,000 people is incorrect. William Lane Craig apparently found it pretty compelling.

  586. 586
    EricMH says:

    Also seems ironic that a forum titled “Peaceful Science” is mostly devoted to tearing down theories that Dr. Swamidass disagrees with.

  587. 587
    ET says:

    As a theistic evolutionist Joshua is a closet IDist. And as a theistic evolutionist he denies that evolution proceeds via blind and mindless processes.

    He lives with a deeply conflicted mind. The only thing that saves him is willful ignorance due to pride.

  588. 588
    ET says:

    But anyway…

    In “Signature in the Cell” Meyer defines “information” basically as it is found in standard and accepted dictionaries:

    the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (such as nucleotides in DNA or binary digits in a computer program) that produce specific effects

    His wording may be slightly different as I pulled that from Merriam-Webster. Both Meyer and Dembski also reference the not-so knightly Francis Crick:

    Information means here the precise determination of sequence, either of bases in the nucleic acid or on amino acid residues in the protein.

    Durston, et al’s Functional Sequence Complexity appears to follow the same definitions.

    In “No Free Lunch” William brings up “discrete combinatorial objects” in reference to irreducible complex biological structures. One of his 3 parts of a DCO is the origin of the parts, which would be the proteins of say ATP synthase. Those proteins are coded for in the DNA.

    The other two parts of the DCO equation are the getting the parts to the right place (at the right time) , ie the localization issue and properly assembling them into the functional unit, ie the configuration issue.

    One thing that stands out is the holistic nature of what is being discussed. It is more than just getting the words of “METHINKS IT IS LIKE A WEASEL”. You need the sentence or you get nothing but a “you tried”.

    The point being is that once we have that we should be able to apply Shannon’s methodology to quantify it.

    OR am I the one totally misreading what these guys- Dembski, Meyer, Durston, et al- are doing?

    OR should I stop reading what Mung has to say about it because he is the one making me question this? 😎

  589. 589
    EricMH says:

    Dr. Swamidass is really committed to the idea that science cannot detect God, similar to the non-overlapping magisteria idea promoted by Stephen Gould in recent history, and related to Averroesism from medieval times.

    My reading is he wants to develop scientific explanations, such as geneological Adam, which are consistent with the Biblical account, but do not prove the existence of God. He also endorses an empirically undetectable guidance of evolution by God, which would not be ID. It is also exhibited by his ‘entropy = information’ claim. This way scientific accounts can stride a neutral zone between atheism and Christianity.

    As such, Swamidass’ agenda is not driven so much by discovering the truth, but to establish ‘peaceful science’ that is consistent with many different sides of the aisle. A ‘methodological neutralism’ or ‘Swiss science,’ if you will.

    It is also why he is against positions like ID that turn out to have much stronger implications if they are true. It is not so much because the evidence is or is not there, but because ID violates the broader agenda of ‘peaceful science’ that is neutral on the big questions. Hence the verbal posturing of giving ID a ‘fair hearing’ but in practice appears to be more about discrediting the intellectual viability of ID, especially on the information theory side, since info theory establishes the validity of design detection on fundamental mathematical grounds, eliminating wiggle room and linguistic ambiguity.

  590. 590
    EricMH says:

    @ET, yes, you are correct. As a software developer, the ID argument from DNA is blindingly obvious. The genetic code is Turing complete, so is the same as any computer code in your favorite language. All programmers know it is next to impossible to generate merely compilable code through a random process, let alone code that does something useful. Even with guidance, as in genetic programming, it is extremely difficult to get decent code that performs some simple task, and requires a fair amount of human intervention along the way. Generating an entire 4D biological organism, not to speak of an entire global ecosystem of such beings, is completely out of the question.

    All of this can be addressed through the FI technique that gpuccio explained to me earlier in the thread, and with standard Shannon and Kolmogorov terminology. Dembski’s CSI is just a more generalized form of these theories, and can incorporate more causal agencies than traditional information theory can.

    Then, of course, there is the whole neglected question of how we get the genetic code in the first place. This also is extremely difficult, especially if we have to start with an analog system.

    And finally, it isn’t even clear that life and mind are Turing reducible, which means there is a fundamental gap between physical laws and life that is impossible to bridge regardless of the infinities of probabilistic resources brought to bear.

    So, if we take off the ideological blinders, ID is just about as brute a fact as there is, in Sean Carroll’s terminology. It is a credit to the materialist PR machine that anyone thinks differently these days.

    At any rate, clearly I should write all this up in formal detail.

  591. 591
    ET says:

    This comment has been removed by the moderator.

  592. 592
    EricMH says:

    @ET, insults like that are not good form. It’s fair to document Swamidass’ discrepancy between claims and practice, but not to insult the person. We should not stoop to the level of our critics.

    From a purely practical standpoint, taking the high ground in debates is more likely to win the audience over than hitting below the belt. It is one of the things that attracted me to ID in the first place, and turned me off the opposition, since ad hominem is a sign the debater’s position is weak.

    The most effective way to defeat an opposing argument is to interpret it in the most charitable way possible, and conclusively show it is still flawed.

  593. 593
    EricMH says:

    I would also add that I believe Dr. Swamidass to be well intentioned and quite a capable computational biochemist. The general intent behind his forum is laudable. However, I think his ‘methodological neutralism’ gets in the way of the unbiased search for truth.

  594. 594
    ET says:

    The following is proof that Joe Feksenstein is totally clueless when it comes to CSI:

    Natural selection can put Functional Information into the genome

    The essay pertains to allele distribution which has nothing to do with CSI. And yet Joe Felsenstein is steadfast in his willful ignorance that he has destroyed the argument that CSI only comes from intelligence.

  595. 595
    EricMH says:

    @ET, I’ll be looking into such arguments in the near or distant future. The answer is probably equivocating the selection function with the solution function.

    For anyone reading this thread, or any other thread I happen through: I’ll make sure all personal insults are removed by mods, and I’ll get repeat offenders banned from UD.

    Uncommon Descent must also be Uncommonly Decent.

  596. 596
    ET says:

    @ EricMH, I have already looked into such arguments and they do not have anything to do with CSI. Any CSI argument would have to do with the origin of the alleles and not their distribution after X generations based on some unrealistic selection function. I don’t even understand how that is information in the context of CSI, especially given that biological specification pertains to function.

    Dembski says that in relation to his Law it is holistic as explained above in 588. As for natural selection, it seems to fair no better than chance: The Strength of Natural Selection in the Wild

  597. 597
    EricMH says:

    I agree. The fallacy with Felsenstein’s example is the specification is tightly coupled to the evolutionary process that generated the alleles. In FI the specification must be selected independently from the evolutionary process.

  598. 598
    EricMH says:

    I’ve been awarded the coveted “worst of the worst of ID” by Tom English. A great honor indeed.

    http://theskepticalzone.com/wp...../#comments

  599. 599
    ET says:

    Tom English also said:

    Eric Holloway is ignoring the fact that Dembski lifted specified complexity — the property of being statistically improbable in a direction specified not with hindsight alone — from Dawkins’s book, without attribution.

    Except that is totally false, on two counts. Leslie Orgel described specified complexity before Dawkins did and on pages 148-9 Dembski quotes Dawkins and references “The Blind watchmaker” with respect to specified complexity. Dembski also references Orgel.

    And Tom doesn’t even understand the argument. If he thinks his “Signature of ID” picture has any “meaning” then he is totally lost, without hope.

  600. 600
    EricMH says:

    Tom English is claiming a function application can increase ASC arbitrarily high. He is making a subtle mathematical error.

    A probability distribution consists of events with labels. A function application changes a label, but does not introduce new events.

    E.g. the sample space of a die roll consists of labelled events {1, 2, 3, 4, 5, 6}. If we apply the function f(x) = x+1 to an event, we don’t change the probability of the event, just the label, i.e. turn the 6 into 7 as in English’s proof. However, English says 7 is a new event that was not contained in the original distribution, and thus has a probability of 0.

    The only way a function application can change probability is by merging labels, e.g. f(x) = 1 labels all the die faces with 1. Thus, when we roll the die we have probability 1.0 of getting a 1. Accordingly, function application can only increase probabilities, not decrease probabilities as is required for English’s argument.

    This means function application can only decrease ASC, at least in the way he is describing, so the non-growth theorem applies to ASC as well.

    Now, the way that function application can increase ASC is if it picks a new x that is more concisely described by the context. This is the way in which the law of non-growth applies in algorithmic mutual information. However, English’s argument is not concerned with this angle.

Leave a Reply