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ID and Common Descent

Many, many people seem to misunderstand the relationship between Intelligent Design and Common Descent. Some view ID as being equivalent to Progressive Creationism (sometimes called Old-Earth Creationism), others seeing it as being equivalent to Young-Earth Creationism. I have argued before that the core of ID is not about a specific theory of origins. In fact, many ID’ers hold a variety of views including Progressive Creationism and Young-Earth Creationism.

But another category that is often overlooked are those who hold to both ID and Common Descent, where the descent was purely naturalistic. This view is often considered inconsistent. My goal is to show how this is a consistent proposition.

I should start by noting that I do not myself hold to the Common Descent proposition. Nonetheless, I think that the relationship of ID to Common Descent has been misunderstood enough as to warrant some defense.

The issue is that most people understand common descent entirely from a Darwinian perspective. That is, they assume that the notion of natural selection and gradualism follow along closely to the notion of common descent. However, there is nothing that logically ties these together, especially if you allow for design.

In Darwinism, each feature is a selected accident. Therefore, Darwinian phylogenetic trees often use parsimony as a guide, meaning that it tries to construct a tree so that complex features don’t have to evolve more than once.

The ID version of common descent, however, doesn’t have to play by these rules. The ID version of common descent includes a concept known as frontloading – where the designer designed the original organism so that it would have sufficient information for its later evolution. If one allows for design, there is no reason to assume that the original organism must have been simple. It may in fact have been more complex than any existing organism. There are maximalist versions of this hypothesis, where the original organism had a superhuge genome, and minimalist versions of this hypothesis (such as from Mike Gene) where only the basic outlines of common patterns of pathways were present. Some have objected to the idea of a superhuge genome, on the basis that it isn’t biologically tenable. However, the amoeba has 100x the number of base pairs that a human has, so the carrying capacity of genetic information for a single-cell organism is quite large. I’m going to focus on views that tend towards the maximalist.

Therefore, because of this initial deposit, it makes sense that phylogenetic change would be sudden instead of gradual. If the genetic information already existed, or at least largely existed in the original organism, then time wouldn’t be the barrier for it to come about. It also means that multiple lineages could lead to the same result. There is no reason to think that there was one lineage that lead to tetrapods, for instance. If there were multiple lineages which all were carrying basically the same information, there is no reason why there weren’t multiple tetrapod lineages. It also explains why we find chimeras much more often than we find organs in transition. If the information was already in the genome, then the organ could come into existence all-at-once. It didn’t need to evolve, except to switch on.

Take the flagellum, for instance. Many people criticize Behe for thinking that the flagellum just popped into existence sometime in history, based on irreducible complexity. That is not the argument Behe is making. Behe’s point is that the flagellum, whenever it arose, didn’t arise through a Darwinian mechanism. Instead, it arose through a non-Darwinian mechanism. Perhaps all the components were there, waiting to be turned on. Perhaps there is a meta-language guided the piecing together of complex parts in the cell. There are numerous non-Darwinian evolutionary mechanisms which are possible, several of which have been experimentally demonstrated. [[NOTE - (I would define a mechanism as being non-Darwinian when the mechanism of mutation biases the mutational probability towards mutations which are potentially useful to the organism)]]

Behe’s actual view, as I understand it, actually pushes the origin of information back further. Behe believes that the information came from the original arrangement of matter in the Big Bang. Interestingly, that seems to comport well with the original conception of the Big Bang by LeMaitre, who described the universe’s original configuration as a “cosmic egg”. We think of eggs in terms of ontogeny – a child grows in a systematic fashion (guided by information) to become an adult. The IDists who hold to Common Descent often view the universe that way – it grew, through the original input of information, into an adult form. John A. Davison wrote a few papers on this possibility.

Thus the common ID claim of “sudden appearance” and “fully-formed features” are entirely consistent both with common descent (even fully materialistic) and non-common-descent versions of the theory, because the evolution is guided by information.

There are also interesting mixes of these theories, such as Scherer’s Basic Type Biology. Here, a limited form of common descent is taken, along with the idea that information is available to guide the further diversification of the basic type along specific lines (somewhat akin to Vavilov’s Law). Interestingly, there can also be a common descent interpretation of Basic Type Biology as well, but I’ll leave that alone for now.

Now, you might be saying that the ID form of common descent only involves the origin of life, and therefore has nothing to do with evolution. As I have argued before, abiogenesis actually has a lot to do with the implicit assumptions guiding evolutionary thought. And, as hopefully has been evident from this post, the mode of evolution from an information-rich starting point (ID) is quite different from that of an information-poor starting point (neo-Darwinism). And, if you take common descent to be true, I would argue that ID makes much better sense of what we see (the transitions seem to happen with some information about where they should go next).

Now, you might wonder why I disagree with the notion of common descent. There are several, but I’ll leave you with one I have been contemplating recently. I think that agency is a distinct form of causation from chance and law. That is, things can be done with intention and creativity which could not be done in complete absence of those two. In addition, I think that there are different forms of agency in operation throughout the spectrum of life (I am undecided about whether the lower forms of life such as plants and bacteria have anything which could be considered agency, but I think that, say, most land animals do). In any case, humans seem to engage in a kind of agency that is distinct from other creatures. Therefore, we are left with the question of the origin of such agency. While common descent in combination with ID can sufficiently answer the origin of information, I don’t think it can sufficiently answer the origin of the different kinds of agency.

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251 Responses to ID and Common Descent

  1. As Dr Behe sated:

    Scott refers to me as an intelligent design “creationist,” even though I clearly write in my book Darwin’s Black Box (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think “evolution occurred, but was guided by God.” Where I and others run afoul of Scott and the National Center for Science Education (NCSE) is simply in arguing that intelligent design in biology is not invisible, it is empirically detectable. The biological literature is replete with statements like David DeRosier’s in the journal Cell: “More so than other motors, the flagellum resembles a machine designed by a human” (1). Exactly why is it a thought-crime to make the case that such observations may be on to something objectively correct?

    Scott blames “frontier,” “nonhierarchical” religions for the controversy in biology education in the United States. As a member of the decidedly hierarchical, mainstream Roman Catholic Church, I think a better candidate for blame is the policing of orthodoxy by the NCSE and others–abetting lawsuits to suppress discussion of truly open questions and decrying academic advocates of intelligent design for “organiz[ing] conferences” and “writ[ing] op-ed pieces and books.” Among a lot of religious citizens, who aren’t quite the yahoos evolutionists often seem to think they are, such activities raise doubts that the issues are being fairly presented, which might then cause some people to doubt the veracity of scientists in other areas too. Ironically, the activity of Scott and the NCSE might itself be promoting the mistrust of science they deplore.

    1. David J. DeRosier, Cell 93, 17 (1998).

    See also:

    biological evolution- what is being debated

  2. This is a very helpful post.

  3. 3

    In its most basic form, all ID says is that some things are designed. Of course that is not incompatible with common descent. That is not incompatible with anything. That’s why people say it’s not scientific.

  4. I don’t see why there is any conflict between ID and common descent, and I don’t think front-loading is a necessary way to reconcile the two. For instance, the designer could have manipulated genes at the moment of conception (or at the moment asexual reproducing organisms split into two), either periodically or always, throughout history from the beginning of life in order to steer births in the direction of the desired evolved change.

    So I don’t see any reason why common descent is in conflict with ID.

  5. In its most basic form, all ID says is that some things are designed.

    Noooo. What ID says is that things that are designed have unique characteristics; these characteristics are quantifiable; and because these characteristics are quantifiable some things can conclusively be shown to have been designed.

  6. Here we get into that classic conflict between two different arguments for design — the fine-tuned universe and abiogenesis. If the universe‘s laws were designed exactly with life in mind, then why should the chemistry derived from those laws be inadequate to result in life, requiring a second instance of design? Bio-ID says the universe we know is inimical to life appearing, phys-ID the opposite.

    If Behe is correct, and all the information needed for evolution was packed into the Big Bang, then how is biological ID necessary? That the designer was responsible for the “extra information” would not make that information “invisible” to non-IDers, would it?

    Also, I’m wondering if any IDer has done studies into the possibility of genome-programmed saltation, or indeed, any genome-programming at all. Normally, all DNA that does not provide immediate function is distorted by mutations, so (it seems) a designer or similar non-natural phenomenon would still be required to shield those genes until they were needed.

    Unless, perhaps, the designing is so good that it can anticipate exactly what every organism and its descendants will encounter at every moment in life, and therefore exactly which mutations will occur where and when.

    Whoa, I think I’ve just invented ID’s Molinism! :)

  7. Lenoxous -

    You are confusing the laws with the arrangements of matter. The arrangement of matter is the information.

    “Here we get into that classic conflict between two different arguments for design — the fine-tuned universe and abiogenesis.”

    I don’t think that those are in conflict. A microcomputer is fine-tuned for holding a program, but it doesn’t itself generate the code for the programs that are run on it. How is there at all a conflict between these two propositions?

    “Bio-ID says the universe we know is inimical to life appearing, phys-ID the opposite.”

    Incorrect. Phys-ID is about the universe creating a safe place for life to exist. Bio-ID is about the life itself.

    “If Behe is correct, and all the information needed for evolution was packed into the Big Bang, then how is biological ID necessary?”

    As mentioned before, this is a confusion between the laws of physics (Phys-ID) and the information content (Bio-ID). Behe’s view is that _both_ the laws of physics _and_ the specific arrangement of matter were made to bring about a specific life. The laws are not sufficient in and of themselves, it requires pre-specified information.

    “Normally, all DNA that does not provide immediate function is distorted by mutations, so (it seems) a designer or similar non-natural phenomenon would still be required to shield those genes until they were needed.”

    That is a Darwinian assumption, but hasn’t really played out all that well. Even if it were true, Yockey showed that Shannon’s laws proved that it could easily be accounted for (I think it was in his paper “Origin of life on earth and Shannon’s theory of communication”).

  8. Nice contribution. I’ ve always been a great supporter of John Davison, it is fine that his work is mentioned.

    I’ve find also Siegfred Scherer’s work very interesting. Basic mammalian bauplans may have arisen de novo, polyphyleticaly. His arguments sound quite convincing.

    Scherer departed from Discovery Institute and his career in Germany seems quite impressive. Anyway he follows ID movement with great sympathy as he wrote in an interview 2 year ago. Some of his interviews can be found at his home page, for those who can read German:

    http://www.siegfriedscherer.de/presse.html

  9. Lenoxus:

    Bio-ID says the universe we know is inimical to life appearing, phys-ID the opposite.

    Do you have a reference for that or are you just talking out of you arse as usual?

    But anyways if you don’t like the design inference all you have to do is to actually strat supporting the claims of your position.

    To date the best “explanation” your position has to offer for the laws that govern this physical realm is-

    “They just are (the way they are)”- Steve Hawking in “A Briefer History of Time”

    And your only “evidence” for your position is the refusal to accept the design inference no matter what.

  10. Walter:

    In its most basic form, all ID says is that some things are designed. Of course that is not incompatible with common descent. That is not incompatible with anything. That’s why people say it’s not scientific.

    ID is incompatible with the current theory of evolution.

    Just read Mayr’s “What Evolution Is”- no teleology allowed.

  11. Joseph:

    In its most basic form, all ID says is that some things are designed. Of course that is not incompatible with common descent. That is not incompatible with anything. That’s why people say it’s not scientific.

    ID is incompatible with the current theory of evolution.

    Once you posit an intelligent designer, all things become possible. It is possible (and theistic evolutionists do this) to imagine a world where the designer starts things and then allows them run their natural course exactly if the designer wasn’t involved. It is also possible to have a designer design things to deliberately look random.

    There may (or may not) be an “Edge to Evolution” – there is no edge to ID.

  12. My comment at #4 is still in moderation, probably because I am new here, so this one may be delayed also, but I’d like to the comment that “ID is incompatible with the current theory of evolution…no teleology allowed.”

    Of course, intelligent design is incompatible with a theory of unintelligent design (the current theory of evolution), but really only with the unintelligent part. The other factors, including slow changes in genomes and common descent, are, as I pointed out in my previous post, are quite compatible with a designer who guides evolution by manipulating events at the moments of conception.

  13. mikev6:

    Once you posit an intelligent designer, all things become possible.

    How so?

    Wouldn’t the designer(s) be limited by physical constraints?

    It is also possible to have a designer design things to deliberately look random.

    We wouldn’t infer design if that were the case.

    Ya see the reason for the design inference is that we do not observe randomness throughout the universe.

    This is all about requirements- as in what is required to produce it.

    If nature, operating freely suffices as an explanation then we do not infer a designer as one is not required.

  14. mikev6 -

    The point is not, “what _could_ the designer do”. The point is “what is there _evidence_ of the designer doing”.

    The evidence is that tissues, limbs, and organs tend to be fully-functional the first time we find them. Whether this happened through common descent or special creation is not evident from the fossils. What is evident is that there was a teleological principle involved in keeping the holistic unity of the organism.

  15. Professor Davison who is mentioned in this incentive article just commented on the issue on his blog. He asked me to inform you about his opinion.
    For those who are interested here is the link:

    http://jadavison.wordpress.com.....mment-2569

    I would recommend also Scherer’s interviews. Thanks to the article I found another scientist with profound independent ideas on the evolution and Christianity. What a fresh air after reading “theistic” speculation at crypto-darwinian venue Biologos.

  16. 16

    tribune7 at 4,

    “In its most basic form, all ID says is that some things are designed.”

    Noooo. What ID says is that things that are designed have unique characteristics; these characteristics are quantifiable; and because these characteristics are quantifiable some things can conclusively be shown to have been designed.

    Excellent, you’ve come to the topic I’ve been trying to discuss since delurking a few weeks ago (lots of threads here go off on very long tangents).

    By “unique characteristics” do you mean Dembski’s Complex Specified Information? If so, do you have an example of CSI being calculated for a real world biological artifact? I’ve read the available literature on CSI but haven’t found such a detailed example.

    My goal in asking is to understand CSI well enough to implement CSI measurement in software, to see if known evolutionary mechanisms are, in fact, unable to generate it.

    If you mean something else by “unique characteristics”, I’d be very interested in hearing more details.

  17. Slightly off topic and sorta icky.
    Evidence of front-loading?
    I doubt it, but it makes one think.

    http://english.pravda.ru/scien.....man_face-0

  18. johnnyb,

    You said “the amoeba has 100x the number of base pairs that a human has, so the carrying capacity of genetic information for a single-cell organism is quite large.” I want to make sure I got this right. Humans have, what, 3 billion base pairs? So amoebas have 300 billion base pairs in their DNA? That sounds unbelievable. I just want to confirm. Thanks!

  19. jasundulle. Yes, see Wikipedia:

    http://en.wikipedia.org/wiki/Amoeba_%28genus%29

    “The amoeba is remarkable for its very large genome. The species Amoeba protea has 290 billion base pairs in its genome, while the related Polychaos dubium (formerly known as Amoeba dubia) has 670 billion base pairs. The human genome is small by contrast, with its count of 2.9 billion base pairs.”

  20. The amoeba is remarkable for its very large genome.

    This is new to me, but on the other hand I’m no biologist. Do we have any idea of why this may be the case?

  21. Mustela Nivalis -

    You are correct that CSI is difficult to quantify in living creatures. That is why most practicing ID has moved on to other notions. You should see Dembski’s current work in active information, and my own work on the relationship between universality and design. These are much easier to use biologically. If you are interested in Dembski’s work, see Dembski’s site. If you are interested in mine, see my recent paper.

  22. johnnyb, are you of the opinion that the concept of “active information” lends itself to quantification in biology? How do we objectively determine the target and the search space?

  23. johnnyb:

    Sometime after I submitted my comment about the “conflict” between phys- and bio-ID, I realized my errors — under ID, life is simply so “out there” that it indeed requires at least two interventions, one for hardware and one for software. Thank you for pointing them out.

    That said, I fail to understand what it meant by the information content of the “arrangement of matter”. Does this mean that (perhaps) the positioning of each particle of the Big Bang was exactly such that bacteria would ultimately develop flagella? Because that’s a pretty darn cool idea. Still, if that were the case, I fail to see why chemists and biologists would need to resort to non-naturalism to account for anything — if the universe was always such that life was guaranteed to occur, then abiogenesis is no problem — and the signs of this “guaranteeing” would be just as visible to naturalists. The initial fine-tuning, of course, would remain an even larger problem, but that’s outside the strictly biological question.

    “Normally, all DNA that does not provide immediate function is distorted by mutations, so (it seems) a designer or similar non-natural phenomenon would still be required to shield those genes until they were needed.”

    That is a Darwinian assumption, but hasn’t really played out all that well.

    I have yet to run across an ID theorist who posits that all mutations are directed. Therefore, I presume that ID accepts that there are at least some random mutations. Therefore, a genome which was “front-loaded” would have to be able to somehow anticipate those random mutations, or be shielded from them. This is not a naturalistic assumption, because it allows for the anticipating or the shielding. (The anticipating I mentioned later, as an afterthought.)

    As for the Hawking quote, I must say that it applies equally to the idea of a designer(s) who just happens to be predisposed to creating life — the designers “just are (the way they are)”. At some point, there’s a final turtle floating in air.

  24. Mustela Nivalis –By “unique characteristics” do you mean Dembski’s Complex Specified Information?

    CSI is certainly a respectable attempt to quantify those characteristics. Does it succeed? I can’t see how it fails but if it should the unique characteristics of design would still remain — which should be obvious — and new attempts would be made to articulate them.

    If so, do you have an example of CSI being calculated for a real world biological artifact?

    I always understood that a chromosome would fit the bill due to the unlikelihood of it coming together by chance and coding for the myriad of complex biological functions that it does.

  25. “johnnyb, are you of the opinion that the concept of “active information” lends itself to quantification in biology? How do we objectively determine the target and the search space?”

    For some circumstances, absolutely. Somatic Hypermutation is a perfect place to look at this. Basically, in your immune system, after recombination of V, D, and J elements, additional mutation occurs to refine the affinity of the antibody to the antigen. A good review of this is here.

    So, basically, during somatic hypermutation, only the antibody is heavily mutated. Likewise, pretty much only the variable region (the region which attaches to the antigen) is mutated and the constant region (the region which attaches to the cell) is not mutated at all. So, the immunoglobulin is about 1,200 nucleotides. The mutation occurs in the right half of the right gene, which limits the scope to about 600 nucleotides. Therefore, a back-of-the-envelope calculation puts the active information in that search at least at about 22 bits. [[ Overly Simplistic (leaning towards fewer bits) Calculation: Log2(base pairs in human genome) - Log2(base pairs in search region) = genome contributes 22 bits to the search]]

  26. “Does this mean that (perhaps) the positioning of each particle of the Big Bang was exactly such that bacteria would ultimately develop flagella?”

    Yes.

    “Still, if that were the case, I fail to see why chemists and biologists would need to resort to non-naturalism to account for anything”

    What about the initial arrangement of atoms?

    “if the universe was always such that life was guaranteed to occur, then abiogenesis is no problem — and the signs of this “guaranteeing” would be just as visible to naturalists.”

    Why? Since it has already occurred, there is no need for those elements to still remain. The problem is that the naturalists assume that the laws themselves can work without information. The origin of self-replication is easy if we can prespecify the arrangements of parts (I say “easy” – “straightforward” is probably a better description).

    The reason naturalists are having problems is that they are unwilling to look at scenarios in which information already existed.

    “Therefore, I presume that ID accepts that there are at least some random mutations.”

    You are correct.

    “Therefore, a genome which was “front-loaded” would have to be able to somehow anticipate those random mutations, or be shielded from them.”

    Yes. Again, see the Yockey paper. I don’t have it in front of me, and if you really need the answer that badly I’ll try to look it up tonight.

  27. Read your excellent paper JohnnyB. Darwinists unlike IDers take for granted the the coordination factor – states that have to be kept track of to produce the holistic effect. A very simple tape player, could be done like so in c:

    #define fastRightState 0
    #define fastLeftState 1
    #define slowLeftState 2
    #define slowRightState 3
    #define stopLeftState 4
    #define stopRightState 5

    state = slowRightState;//initial start state

    int main(void) {

    while(1) {

    switch(state) {

    case stopLeftState:
    if(key_control(0)) {
    state = slowLeftState;
    }
    else {
    //stopSideA();
    }
    break;

    case stopRightState:
    if(key_control(0)) {
    state = slowRightState;
    }
    else {
    //StopSideB();
    }
    break;

    case slowLeftState:
    if(key_control(1)) {
    state = stopLeftState;
    }
    else if(key_control(3)) {
    state = slowRightState;
    }
    else if(key_control(2)) {
    state = fastRightState;
    }
    else {
    //PlaySideA();
    }
    break;

    case slowRightState:
    if(key_control(1)) {
    state = slowRightState;
    }
    else if(key_control(3)) {
    state = slowLeftState;
    }
    else if(key_control(2)) {
    state = fastLeftState;
    }
    else {
    //PlaySideB();
    }
    break;

    case fastLeftState:
    if(key_control(0)) {
    state = slowRightState;
    }
    if(key_control(1)) {
    state = stopRightState;
    }
    if(key_control(3)) {
    state = fastRightState;
    }
    else {
    //RewindSideA();
    }
    break;

    case fastRightState:
    if(key_control(0)) {
    state = slowLeftState;
    }
    if(key_control(1)) {
    state = stopLeftState;
    }
    if(key_control(3)) {
    state = fastLeftState;
    }
    else {
    //RewindSideB();
    }
    break;

    default:
    //
    break;
    }
    }
    }

  28. johnnyb:

    “Still, if that were the case, I fail to see why chemists and biologists would need to resort to non-naturalism to account for anything”

    What about the initial arrangement of atoms?

    If there is nothing inherently non-naturalistic about those atoms and their arrangement, then naturalism is free to postulate and “study” them (in a theoretical sense). Physicists right now are trying to work out what the initial moments of the Big Bang were like, down to the tiniest detail. Naturalism does not hamper them in doing so.

    That a designer might be required for that atomic arrangement to have existed in no way precludes one from naturalistically finding such an arrangement to have existed — the arrangement would not be “invisible” to naturalism, because, despite its origin, it would have solely natural properties. I might refuse to believe that trees produce sap, but that won’t render me incapable of sensing and studying maple syrup — I’ll just have an alternate hypothesis for its origin (or call its existence a brute fact).

    I guess what I’m trying to figure out is, if all the info was “statically” there from the beginning, with no further design involvement required, then why shouldn’t naturalists be able to develop theories regarding this initial arrangement? Because evo-biologists, despite what they might claim, can’t actually ever believe in “information”?

  29. “then why shouldn’t naturalists be able to develop theories regarding this initial arrangement?”

    There’s no reason why they _couldn’t_, but the motivation for naturalism is to avoid such implications.

  30. Mustela Nivalis- aka weasel man,

    My goal in asking is to understand CSI well enough to implement CSI measurement in software, to see if known evolutionary mechanisms are, in fact, unable to generate it.

    “Evolutionary mechanisms” don’t have anything to do with it.

    Blind and undirected processes is what ID argues against.

    To measure information in biology just see what is required functionality.

    Then if enough information is required (500 bits) then CSI is present.

    However all that is moot because all YOU have to do is demonstrate that blind and undirected processes can account for it- IOW all you have to do is to actually start substantiating the claims made by YOUR position and ID would go away.

    So why don’t you people just go out and do that?

  31. Lenoxus,

    ID is about the DESIGN not the designer.

  32. Joseph:

    Wouldn’t the designer(s) be limited by physical constraints?

    Not necessarily. The goal of this site is to ensure that science includes both the material and non-material – the concern being that considering only the material may lead us to miss the right answer in searching for explanations. We have to be open-minded enough to consider an agent or agents that either transcends the material or is so technologically advanced that it seems so to us.

    If nature, operating freely suffices as an explanation then we do not infer a designer as one is not required.

    Ahh, so if Nature can explain it, then it’s Natural; otherwise, Design? What if there’s an explanation from Nature we haven’t found yet? How would we distinguish the two? And how is this not an “ID-of-the-gaps” argument?

    In the original post it was suggested that ID can support both common descent and “not-common descent”. Those are pretty much mutually exclusive explanations – which one does ID fit better? If the answer is “both” then we’re back to the thought that it’s so broad that it can explain anything.

  33. johnnyb:

    The evidence is that tissues, limbs, and organs tend to be fully-functional the first time we find them.

    I’ll remember this the next time I break my tailbone. :-)

    Whether this happened through common descent or special creation is not evident from the fossils. What is evident is that there was a teleological principle involved in keeping the holistic unity of the organism.

    So is there any organization of the fossil record that ID doesn’t support? I could argue that the order of speciation was determined by alphabetical order and ID would still support that too.

  34. mikev6:

    So is there any organization of the fossil record that ID doesn’t support?

    ID is silent on the fossil record.

    Wouldn’t the designer(s) be limited by physical constraints?

    Not necessarily.

    Yet all designers are so constrained.

    The goal of this site is to ensure that science includes both the material and non-material – the concern being that considering only the material may lead us to miss the right answer in searching for explanations.

    The debate is blind and undirected vs purposeful and directed processes.

    If nature, operating freely suffices as an explanation then we do not infer a designer as one is not required.

    Ahh, so if Nature can explain it, then it’s Natural; otherwise, Design?

    No- first I did NOT say “nature”.

    Can Nature explain itself?

    However if nature, operating freely can account for something then we do not infer design because there isn’t any requirement for a designer.

    What if there’s an explanation from Nature we haven’t found yet? How would we distinguish the two? And how is this not an “ID-of-the-gaps” argument?

    Science does not and cannot wait for what the future may of may uncover.

    Scientists have to go with the current level of knowledge available.

    Also to reach a design inference it is not enough that nature, operating freely cannot account for it.

    There also has to be a specification.

    This is all in “The Design Inference” and “No Free Lunch”- it’s called the explanatory filter.

    In the original post it was suggested that ID can support both common descent and “not-common descent”.

    ID is silent on the matter of Common Descent.

  35. Mustela Nivalis –My goal in asking is to understand CSI well enough to implement CSI measurement in software, to see if known evolutionary mechanisms are, in fact, unable to generate it.

    Start with the symbols used by the programming language of your choice, generate them randomly, when you get something that compiles, latch it and continue. Let us know how you do :-)

  36. johnnyb @ 24, thank you for answering with a quantitative example. It’s refreshing to be dealing with specifics.

    Log2(base pairs in human genome) – Log2(base pairs in search region) = genome contributes 22 bits to the search

    Pardon my ignorance of biology, but I don’t see what’s being calculated here. If the first term is the endogenous information, then that would indicate that the search space is the set of base pairs in the genome (approx 3,000,000,000?) and that the target is a certain base pair. If the second term is the exogenous information, then that would indicate that the active information in question reduces the search space from the whole genome to 600 base pairs. Am I on the right track?

  37. I don’t see a large philosophical or theological gap between theistic evolution and common descent ID. What does common descent ID demand theologically that theistic evolution will not allow?

  38. mikev6 (), “There may (or may not) be an “Edge to Evolution” – there is no edge to ID.”

    First, what’s with the “or may not” bit? Are you not giving naturalism a way out? Is naturalism testable as long as “or may not” is part of the statement?

    Put this into your naturalistic pipe for a bit:

    The HAR1F gene is different in 18 non-contiguous point mutations in humans than it is in non-human animals.

    Within the vertibrates the thing is painfully consistent, where there are three point mutations that seem to be “unlocked”, and wander between species, but the other 100 or so mutations are always the same.

    As Behe has demonstrated that even a pair of simultaneous mutations is beyond the reasonable edge of evolution, how do you explain 18 points.

    Oh, I know, you argue that they may not have been simultaneous. However, we have the evidence of all of those other vertibrates to show that all single point mutations must be deleterous. Further, the lock and key nature of the gene’s folding requires that the mutations, or at least a majority of them, had to have happened simultaneously.

    That, my friend, falsifies a naturalistic explanation. The only way I can see to get from animal HAR1F to human HAR1F is with a technique called “strategy”. That’s how we humans do it.

  39. 39

    tribune7 at 23,

    “If so, do you have an example of CSI being calculated for a real world biological artifact?”

    I always understood that a chromosome would fit the bill due to the unlikelihood of it coming together by chance and coding for the myriad of complex biological functions that it does.

    Can you point me to an example of where someone has calculated the CSI of a chromosome?

    By the way, no biologist would suggest that a modern chromosome came together by chance. Any valid calculation of CSI would need to take into account known evolutionary mechanisms.

  40. 40

    johnnyb at 20,

    You are correct that CSI is difficult to quantify in living creatures. That is why most practicing ID has moved on to other notions. You should see Dembski’s current work in active information, and my own work on the relationship between universality and design. These are much easier to use biologically. If you are interested in Dembski’s work, see Dembski’s site. If you are interested in mine, see my recent paper.

    Thanks for the references. What I’m looking for is a precise, quantifiable definition of how design can be detected. CSI seems to be the recommended metric for most in the ID community. Do you have another? (Active information hasn’t been applied to an actual biological artifact, as far as I know).

  41. “ID is silent on the fossil record.”

    http://www.discovery.org/a/1772

    I didn’t believe ID was silent on the fossil record. How can someone say that unless they did not know about the article referenced in the link above?

  42. 42

    tribune7 at 34,

    Mustela Nivalis –”My goal in asking is to understand CSI well enough to implement CSI measurement in software, to see if known evolutionary mechanisms are, in fact, unable to generate it.”

    Start with the symbols used by the programming language of your choice, generate them randomly, when you get something that compiles, latch it and continue. Let us know how you do

    I need a quantifiable, implementable definition of CSI first. Otherwise I won’t know if any has evolved.

    However, John Koza, among many others, has been doing some interesting work similar to what you describe.

  43. R0b:

    “then that would indicate that the active information in question reduces the search space from the whole genome to 600 base pairs. Am I on the right track?”

    Precisely.

    Mustela Nivalis -

    “CSI seems to be the recommended metric for most in the ID community. Do you have another?”

    I gave an example of active information applied for R0b above. I have my own “metric” (it’s actually currently qualitative, not quantitative, but I still think it is quite usable), which I apply to a subsystem of the bacterial flagellum in this paper. The application is in section 3.1. The nice thing about my metric is that it lends itself to applications beyond just determining what is designed and what is not.

  44. Mustela said, “By the way, no biologist would suggest that a modern chromosome came together by chance. Any valid calculation of CSI would need to take into account known evolutionary mechanisms.”

    Evolutionary mechanisms are chance. It’s merely chance one step removed. Chance means that there was no intentionality at one end. Putting a pattern between chance and outcome does not make it not chance.

  45. johnnyb,

    Thanks for the confirmation on amoebas. While ID theorists believe that “junk DNA” has function, surely not all of it can have function. If it did, we would expect for the amoeba to be more complex than humans since it has so much more code, and yet that’s not true. Would you say that the genome of the amoeba got so large due to random mutations (and lots of them)?

  46. Mustela – Any valid calculation of CSI would need to take into account known evolutionary mechanisms.

    And, specifically, what are they?

  47. 47

    johnnyb at 43,

    I have my own “metric” (it’s actually currently qualitative, not quantitative, but I still think it is quite usable)

    Any metric that purportedly can be used to identify design must be quantitative and objective. If such a metric exists, any observer must be able to measure it and come to the same conclusion (within the bound of experimental error).

    CSI has been presented as such a metric. I’ve read all the literature I can find, but have been unable to turn up a worked example for a real biological system. Do you have any plans to make your qualitative approach more mathematically rigorous?

  48. Mustela –Otherwise I won’t know if any has evolved.

    When you compile you know you are having success in your evolution.

    However, John Koza, among many others, has been doing some interesting work similar to what you describe.

    Unless you can identify naturally occurring algorithms you may not use them in your evolution project if you want to be faithful to nature.

  49. 49

    Collin at 44,

    Mustela said, “By the way, no biologist would suggest that a modern chromosome came together by chance. Any valid calculation of CSI would need to take into account known evolutionary mechanisms.”

    Evolutionary mechanisms are chance. It’s merely chance one step removed. Chance means that there was no intentionality at one end. Putting a pattern between chance and outcome does not make it not chance.

    Mutations are random, selection is not.

  50. 50

    tribune7 at 46,

    Mustela – “Any valid calculation of CSI would need to take into account known evolutionary mechanisms.”

    And, specifically, what are they?

    Allen MacNeill supplied a list of some awhile back.

    Do you have an example of CSI calculated for a real biological artifact?

  51. johnnyb, I’m afraid I still don’t understand your example. What base pair does the process search for, and how did you determine that this base pair is the target?

  52. Mutations are random, selection is not.

    One could imagine how selection might favor a new feature, such as an eye or a wing. How does selection favor a single mutation, the first step in a series of mutations that will eventually lead to some tangible benefit?
    Apparently selection not only isn’t random, but it exercises foresight and planning. It sees and protects unexpressed potential until it forms something useful.

  53. Selection is random, but its randomness is once removed. The environment that favors a mutation came into existence either by random processes or by intent of someone/something. It is therefore random. To say otherwise is magical thinking.

  54. By the way, no biologist would suggest that a modern chromosome came together by chance . . .Allen MacNeill supplied a list of some awhile back.

    Two points:

    1. Those mechanisms are ultimately effects of chance according to Darwinism but that doesn’t really matter because . . .

    2. All those mechanisms depend on the pre-existence of chromosomes.

    So it seems that chromosome stands as example of a biological entity exhibiting CSI since it has complex specificity and the probability of it occurring by chance is greater than 1 in 10^150.

  55. Mustela, 54 was for you.

  56. tribune7,

    Good point. I never understand when darwinists say, “Natural selection is the engine of evolution.” That is totally irrational! Natural selection only destroys. It can never create.

  57. I think I am repeating what someone else said, but nobody believes that the first chromosome (or its precursors) happened strictly “by chance”. Chance events always happen in the larger context of natural laws – chance provides the variation but the main structures of what happen are provide by the interplay of natural laws.

    So even though it may be correct to say that the probability of a chromosome “occurring by chance is greater than 1 in 10^150,” that doesn’t mean that the probability of a chromosome occurring through a chain of natural events is greater than 1 in 10^150.

  58. R0b:

    The reason I said my estimates were low is because it is based on a single base pair needing change. I don’t know the numbers, but my guess is that it is more than that (actually, even more because a nucleotide has four possible values, and I calculated it for 2).

    The pair that it searches for is the one that increases binding strength to the antigen. The way I determined that this was the target is because the threat is the antigen.

  59. Mustela Nivalis -

    Why must it be quantitative to be objective? Qualitative analysis in chemistry is objective, but it isn’t quantitative. Why don’t you read the paper and then criticize the method specifically, rather than complaining about it generally?

    jasondulle -

    I know nothing about the contents of the amoeba genome. My only point about the amoeba was simply that the maintenance of a large genome for a common ancestor is not a theoretical problem.

    However, I will take issue with this statement:

    “If it did, we would expect for the amoeba to be more complex than humans since it has so much more code”

    This does not follow. Take, for instance, the Windows installer program. It has _more_ code than Windows, but it is less complex, because it’s job is to move the Windows operating system to the right location (your hard drive). Taking a biological example, a zygote is less complex than a human, but they both contain the same genetic information. Therefore, if ontogeny is a model of phylogeny (as, for instance, Davison believes) then it makes sense that there would be a lot of unexpressed code waiting for the right time to activate.

  60. 60

    tribune7 at 54,

    So it seems that chromosome stands as example of a biological entity exhibiting CSI since it has complex specificity and the probability of it occurring by chance is greater than 1 in 10^150.

    Could you please show your work? What is the objective specification? How, exactly, is CSI calculated? How are you relating a measure of information (CSI) to a probability?

  61. 61

    Aleta at 57,

    So even though it may be correct to say that the probability of a chromosome “occurring by chance is greater than 1 in 10^150,” that doesn’t mean that the probability of a chromosome occurring through a chain of natural events is greater than 1 in 10^150.

    Very well put.

  62. 62

    johnnyb at 59,

    Why must it be quantitative to be objective? Qualitative analysis in chemistry is objective, but it isn’t quantitative.

    In chemistry, the term “qualitative” in “qualitative analysis” has a specific meaning. The testing that follows qualitative analysis is quantitative.

    I’m looking for the equivalent of that test for ID. What measurement can be made to decide whether or not a particular biological artifact was designed?

  63. Mustela Nivalis -

    So… are you going to read the paper?

  64. Aleta said,

    “So even though it may be correct to say that the probability of a chromosome “occurring by chance is greater than 1 in 10^150,” that doesn’t mean that the probability of a chromosome occurring through a chain of natural events is greater than 1 in 10^150.”

    I certainly don’t understand this reasoning. That would make the first assertion totally meaningless. Do you think that the person who gave us the 1 in 10^150 assertion was assuming that no natural laws existed? Of course not.

    The assertion is that the chance of a chromosome being assembled by undirected, natural processes is 1 in 10^150.

  65. Aleta –Chance events always happen in the larger context of natural laws

    What are the natural laws to that cause a chromosome to form?

  66. 66

    johnnyb at 63,

    So… are you going to read the paper?

    I glanced through it. Unfortunately, I saw nothing that would demonstrate how to objectively identify design in a real biological system. If I missed that information, please summarize it or cite the specific section where it is documented.

  67. 67

    Collin at 64,

    The assertion is that the chance of a chromosome being assembled by undirected, natural processes is 1 in 10^150.

    That is my understanding of tribune7′s assertion as well. I would like to see the actual calculations that support that assertion.

  68. Mustela,

    Indeed, I don’t have them. Nor do I know how they were arrived at. It could be totally falacious for all I know.

  69. See sections 2.5, 2.6, and 3.1. See also its application to an objectively designed system in 3.4.

  70. As far as the list of “evolutionary mechanisms” Allen MacNeill has provided-

    “Evolutionary mechansims” are a conflation, meaning they are not necessarily blind and undirected.

    Dr Spetner goes over this in “Not By Chance” which came out in 1997.

  71. Mustela Nivalis:

    Unfortunately, I saw nothing that would demonstrate how to objectively identify design in a real biological system.

    And what is there to objectively identify illusory design in a real biological system?

    But I digress-

    The criteria for inferring design in biology is, as Michael J. Behe, Professor of Biochemistry at Leheigh University, puts it in his book Darwin ‘ s Black Box:

    “Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”

    He goes on to say:

    ” Might there be some as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would work. Further, it would go against all human experience, like postulating that a natural process might explain computers.”

  72. Mustela Nivalis -What is the objective specification?

    The chromosomes code for a myriad of specifics much of which are directly related to the survival of the individual or the species. Do you need examples?

    How, exactly, is CSI calculated? How are you relating a measure of information (CSI) to a probability?

    –It’s not me that’s relating a measure of information to probability but Dembski.

    –Probability is intrinsic to calculating CSI.

    –Probability calculations are inherently part of information theory.

    What is your problem with using probability calculations in attempting to determine design?

  73. Collin back at #64 seems to be saying that the statement that “the probability of a chromosome occurring by chance is greater than 1 in 10^150″ is the same as “the chance of a chromosome being assembled by undirected, natural processes is 1 in 10^150.”

    This seems to imply that “by chance” and “by undirected, natural processes” mean the same thing, but that doesn’t make sense to me, as “undirected natural processes” include a great deal more than just chance events.

    That’s why I wrote ““So even though it may be correct to say that the probability of a chromosome “occurring by chance is greater than 1 in 10^150,” that doesn’t mean that the probability of a chromosome occurring through a chain of natural events is greater than 1 in 10^150”, which I believe is correct.

    The bigger issue here is how do things in general happen, and the related issue is how could one calculate the probability of them happening? All events have a long causal history – a confluence of many threads coinciding together to cause the event. Often some of those threads have no causal dependence on some of the other threads, so we say that their intersection at the moment of the event is “by chance”. That doesn’t mean that the entire event was “by chance” – it merely means that some of the many causal chains were not themselves causally connected to each other.

    That is why I don’t think “by chance” and “by natural processes” mean the same things, and it’s why I don’t think calculations of the probability of events can be accomplished by just assuming that everything happened by chance.

  74. Aleta–That is why I don’t think “by chance” and “by natural processes” mean the same things,

    So you have faith that there are natural processes that cause certain things to form beyond blind chance?

  75. Aleta,

    We certainly have a different idea of what chance is. I see a person hit by lightning as a random event that happened by chance and yet was also by natural processes. Do you disagree?

    I think that everything not done with the intention of a person is a chance process, even uniform patterns. They came about by chance or in other words, undirected, unintended. How is the existence of the universe not by chance or the current make up of the universe. It seems to me (and tell me if you think this is a false dichotomy) that you have two kinds of events only: actions of agents who intend it and those that are random, by chance.

    It just seems like evolutionists want to make it seems like mutations are not random and that magically they are somehow able to overcome the problems with deleterious mutations being the vast majority of mutations around.

  76. Thanks for the reply Collin. You write, “I think that everything not done with the intention of a person is a chance process, even uniform patterns. They came about by chance or in other words, undirected, unintended. … It seems to me (and tell me if you think this is a false dichotomy) that you have two kinds of events only: actions of agents who intend it and those that are random, by chance.”

    Yes, I do think this is a false dichotomy, but it is illuminating to me for you to state the case so clearly, and it helps me understand what you wrote above: you do see “by chance” as equivalent to “by natural processes” because you see the key criterion is whether the event was direct or undirected.

    But I don’t think this is a proper use of the idea of chance. For instance, suppose it rains hard on a mountainside and the resulting erosion causes a mudslide: this is certainly undirected, but the overall event is caused by operation of the laws of physics and chemistry. It makes no sense to me to say that this was a chance event just because it wasn’t intended by an agent.

    But then you write, “We certainly have a different idea of what chance is. I see a person hit by lightning as a random event that happened by chance and yet was also by natural processes. Do you disagree?”

    No I don’t disagree with this, but this is different than what you said above. The chance part of things is that the person just happened to be where the lightning bolt hit. We call this “random” because there is no causal connection between the lightning bolt (which has a short natural causal history leading up to hitting the ground) and the history of the person which happened to put him under the lightning bolt. The intersection of those two events was “by chance”, but that doesn’t mean that the whole set of events should be said to be “by chance”.

    What interests me is that we (people in general, I think) don’t have a clear idea of what we mean by words like “chance”, “random”, “contingent”, etc., nor of the role that “chance” plays as natural processes flow from one moment to the next. That’s why I think this is an interesting topic.

    P.S.

    Tribune7 writes, “So you have faith that there are natural processes that cause certain things to form beyond blind chance?”

    Sure, although saying I have “faith” is the wrong way to put it. I am quite confident that there are natural processes that cause lightning bolts to form, for instance, and that we (especially those that study these matters closely) know quite a bit about how natural processes cause lightning bolts to form. I can’t imagine anyone believing that lightning bolts are caused by pure chance.

  77. johnnyb, thanks for the clarification. The questions still remain: How did you determine that the target is a base pair that plays a role in countering a certain threat? (Maybe the DNA belongs to Hitler, and the “best” outcome would be a different set of mutations that would hopefully kill him.) And how did you determine that the search space is the entire genome?

    The point I’m trying to make is that Marks and Dembski’s framework doesn’t tell us how to determine these things. It assumes that a mathematical model, including a search space and target, is given. If we want to measure the active info in an observed physical process or system, we have to model it first, and our choices in modeling it determine how much active info is in it. So it seems that to make active info an objective measure of physical phenomena, Marks and Dembski need to define some constraints that determine how phenomena are modeled.

    And this isn’t just a problem for physical systems. I can show how different ways of applying the active info framework to Scheider’s ev yield different values for active info.

  78. 78

    Regarding the odds of the formation of chromosomes, etc. Aren’t the odds dependent on the situation? The odds that a human being will develop from two randomly selected cells placed in a petri dish are pretty small. But if you take one sperm and one egg cell, and they are placed inside a human female’s reproductive system, the odds are probably different.

    So tribune7, when you state that the odds of some event occurring are 1 in ten the one hundred fiftieth power, what is the initial situation in which the chromosome is to occur?

  79. Aleta — I am quite confident that there are natural processes that cause lightning bolts to form,

    That’s a fair point.

    I’ll rephrase my statement to say that you have faith there are natural processes that cause chromosomes to form beyond blind chance :-)

    A question — why would you dismiss design?

  80. “If we want to measure the active info in an observed physical process or system, we have to model it first, and our choices in modeling it determine how much active info is in it.”

    I don’t see how it is so arbitrary. Standard mutational theory says, “whether a particular mutation happens or not is unrelated to how useful that mutation would be.”

    Active information shows that, in the case of Somatic Hypermutation, this statement is incorrect by approximately 22 bits. I didn’t understand your issue with the example, except that your issue seemed contrived (which wouldn’t be so much a problem, except I didn’t understand your point).

    It is always true that anything that you say about a physical system depends on how you model it. That is true for anything. I don’t see how it is specific to this issue. The only difference is that in this case the analogy from the model to the system is pretty well-defined, since there is a static information store, and the trigger for the mutation is the antigen, and the mutation happens in the right half of the right gene.

    Anyway, I am unclear how the parameters for the demarcation of the search space that I used are surprising or unsupported. The genome has been very clearly identified as an information system by nearly every biologist who has ever looked at it. In addition, the genome includes both the sequence before it is modified and the sequence after it is modified. So, the question is whether or not the cell has information to help itself out. Therefore, the reference information space would be the genome of the cell in question. The 22 bits are the amount of help that the cell’s internal information contributes to refining the search for a better antibody. It seems rather straightforward to me. Do you have an alternate suggestion as to what the search space should be?

  81. To Collin: here’s a simpler example.

    An apple disconnects from a tree and falls straight down under the influence of gravity. This did not happen by intent, so according to the dichotomy you suggested in 75 this falling would be a chance event.

    That, of course (it seems to me) makes no sense. Falling is caused by a well-known natural phenomena regarding the attraction of masses, and it happens with such great regularity that we can formulate very precise rules that describe the relationship between the masses and the falling of the object. There is very little of what anyone would consider chance going on in this situation.

  82. Aleta,

    But there is no causal connection between the apple and the ground. Or at least there is as much as between the person and the lightning bolt. After all, there must be electrical potential between the person and the clouds. I really think that under your reasoning there is no such thing as chance. And you know, maybe there isn’t. I mean, if somebody knew everything, then for that somebody, there would be no chance.

  83. …actions of agents who intend it and those that are random, by chance.

    There are a couple of fallacies here.

    For one, in the case of agents and their intentions you are talking about them agents as a cause, yet chance is not a cause of anything.

    See:

    Not a Chance: The Myth of Chance in Modern Science and Cosmology

  84. Mustela Nivalis:

    Unfortunately, I saw nothing that would demonstrate how to objectively identify design in a real biological system. If I missed that information, please summarize it or cite the specific section where it is documented.

    And yet I’d wager that you think that natural selection can imitate design. What is the objective basis of this belief? iow, you have to have a rational basis for this belief (one would hope), but that would mean that you have an objective way of identifying “design.” Else how can you claim that it can be imitated by natural selection?

    If I missed that information, please summarize it or cite the specific section where it is documented.

    Uri Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapter 3, Section 3.2. Page 27.

    Satisfied?

  85. Alerta:

    An apple disconnects from a tree and falls straight down under the influence of gravity.

    Did you realize that the laws that govern this physical realm are evidence for design?

  86. Walter Kloover –Aren’t the odds dependent on the situation?

    Yes, they are. Now what are the factors of nature that bring the odds of the formation of the chromosome beneath the Universal Probability Bound? The UPB, btw, is a standard far higher than what we use in a daily practical sense to determine design.

    And remember your initial point back in Post 3 to which I responded –In its most basic form, all ID says is that some things are designed — ID is not about making a philosophical claim but about science.

    ID is an attempt to objectively discern design in the physical world. The ID claims using methodologies based on CSI and IC are potentially falsifiable.

    For instance, laws of nature, may be found that drastically cut the probability for the formation of chromosomes showing them to conclusively not have CSI.

    But to say that they will be found hence ID can be ignored is not really very scientific, is it?

    That ID is potentially falsifiable, btw, is very strong reason not to put your faith in God in it, and in no way am I suggesting, unlike the Darwinists with their philosophy, that ID be considered a dogmatic truth.

  87. 87

    tribune7 at 72,

    Mustela Nivalis -”What is the objective specification?”

    The chromosomes code for a myriad of specifics much of which are directly related to the survival of the individual or the species. Do you need examples?

    Yes, I would like to see an explicit, worked example of how to calculate CSI for a real biological system or component.

    Do you have one?

  88. Mustela Nivalis — The chromosomes code for a myriad of specifics much of which are directly related to the survival of the individual or the species. Do you need examples . . .Yes

    The nervous system and the reproductive system.

  89. 89

    Mung at 84,

    Mustela Nivalis:

    “Unfortunately, I saw nothing that would demonstrate how to objectively identify design in a real biological system. If I missed that information, please summarize it or cite the specific section where it is documented.”

    And yet I’d wager that you think that natural selection can imitate design.

    That’s a red herring. I’m trying to understand the objective, positive evidence for ID. From my reading, it appears that CSI, as described by Dembski in No Free Lunch, is a major component of that evidence. I have thus far not been able to find any examples of CSI being calculated for a real biological system or component, hence my asking for such an example here.

    My beliefs are unimportant, I just want to understand CSI in enough detail to write software to measure it.

    “If I missed that information, please summarize it or cite the specific section where it is documented.”

    Uri Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapter 3, Section 3.2. Page 27.

    Satisfied?

    No. Unless you are asserting that your citation references a worked example of CSI calculated for a real biological system, it doesn’t address the claim of tribune7 at 5:

    What ID says is that things that are designed have unique characteristics; these characteristics are quantifiable; and because these characteristics are quantifiable some things can conclusively be shown to have been designed.

    What, exactly, are these unique characteristics? How can they be quantified? Can they be proven to be a reliable indicator of intelligent design?

  90. 90

    tribune7 at 88,

    The nervous system and the reproductive system.

    That is not a worked example of how to calculate CSI for a real biological system or component.

    Do you have one?

  91. 91

    johnnyb at 69,

    See sections 2.5, 2.6, and 3.1. See also its application to an objectively designed system in 3.4.

    Thanks for the references.

    As it stands, and as you forthrightly recognize in your paper, you have not yet identified a mechanism, either quantitative or qualitative, for reliably identifying design in a biological system. I look forward to reading your future papers as you further explore this area.

  92. Mustela:

    As it stands, and as you forthrightly recognize in your paper, you have not yet identified a mechanism, either quantitative or qualitative, for reliably identifying design in a biological system.

    Drs Behe, Dembski and Meyer ahve done just that.

    IOW as it stands you are ignorant of ID and you think your ignorance is some sort of refutation.

    Strange.

    Also the “claculation” part was to figure out the UPB.

    Once that is done you measure the amount of information present to see if CSI is also present.

    And in the end you need not worry about CSI nor anything ID.

    Ya see weasel man all YOU and your ilk have to do is demonstrate that which IDists claim is designed can arise without agency involvement.

    IOW YOU need to produce a worked example of a complex biological system arising via blind and undirected processes.

  93. To Collin at 82:

    You say that “There is no causal connection between the apple and the ground.”

    The causal connection between the apple and the ground is the force of gravity. I don’t see how you can say there is no causal connection.

    You write, “I really think that under your reasoning there is no such thing as chance.”

    I don’t see why you would think that. I clearly stated above one common meaning of chance: when two causally independent chains of event intersect, such as when a lightning bolt strikes a person. Such “chance” interactions are an essential part of the world.

    And you write, ” And you know, maybe there isn’t [such a thing as chance]. I mean, if somebody knew everything, then for that somebody, there would be no chance.”

    That’s exactly the position some people take about God, including, I believe RC Sproul, who tribune links to in another post. But that’s not very relevant to us, mere mortals that we are. We’re not omniscient, and to us there will always be chance events in the sense I’ve mentioned them.

    to Tribune at 79 (but I notice that post numbers change which is inconvenient)

    You write, “I’ll rephrase my statement to say that you have faith there are natural processes that cause chromosomes to form beyond blind chance A question — why would you dismiss design?”

    Working backwards, I haven’t even mentioned design, much less dismissed it. I’m focusing on the issue of how natural processes work, and in particular on Collin’s assertion that the dichotomy that things are either caused by an agent or by pure chance, my point being that nothing happens by pure chance – chance takes place in a much larger context of the operation of natural laws.

    Also, I changed the focus of the discussion (for me) from something that happened billions of years ago (the origin of chromosomes) to things that happen right now (apples falling, lightning striking, instead) to better illuminate the issue of interest to me: the nature of the causes of events.

  94. Alerta:

    chance takes place in a much larger context of the operation of natural laws.

    And how did those laws arise if not by chance?

  95. Mustali — That is not a worked example of how …

    It is answer to the question I posed in 72.

    I’m starting to suspect you are a bit of a troll but since a conclusive determination can’t be made outside the UPB, I’ll give you this:

    The smallest chromosome is that of the Candidatus Carsonella ruddii, a bacteria, at 159,662 base pairs. For the four bases of DNA to arrange themselves by chance into a specific sequence of 159,662 base pairs is far, far beyond the UPB. I’d give you a number but my calculator doesn’t go that high.

    Now, you might want to challenge the specificity saying the structure would work adequately if this condon was where that condon was; or you might want to bring down the odds a bit by saying the structure would work absent this set of condons, but you are still not going to do it enough to come close to getting beneath the UBP, nor are you going significantly dent the need for a complex specificity.

    So you are going to resort to saying there must be an undiscovered necessity that causes the chemicals to self-organize in such a fashion.

    This is basically resorting to faith to rebut Dembski’s science.

    Now, you might go out and do the hard work of finding and demonstrating such a necessity but that is much different than yapping about how it is contingent on us to show that one does not exist.

    As it stands now, Dembski’s model is the best description of nature. Perhaps, that will change but such is science.

    BTW, the Candidatus Carsonella ruddii is endosymbiotic — it depends on a host for survival. It’s certainly not a starting place for evolution.

  96. Aleta –to better illuminate the issue of interest to me: the nature of the causes of events.

    Classically, events result from either law, chance or design. I certainly don’t deny the existence of law or chance. ID is just an attempt to separate design from them.

  97. 97

    tribune7 at 95,

    The smallest chromosome is that of the Candidatus Carsonella ruddii, a bacteria, at 159,662 base pairs. For the four bases of DNA to arrange themselves by chance into a specific sequence of 159,662 base pairs is far, far beyond the UPB. I’d give you a number but my calculator doesn’t go that high.

    Please just provide the formula, then. If you’re suggesting that the CSI of that chromosome is simply the number of bits required to identify one of the four bases raised to the power of the length of the chromosome (e.g. 2^159662) then you are failing to take into account known evolutionary mechanisms. No biologist would suggest that such a chromosome came together spontaneously and de novo.

    You also haven’t provided a definition of the specification of the chromosome.

    Do you or don’t you have an example of how to calculate CSI, as described by Dembski in No Free Lunch for a real biological system?

  98. Interestingly, tribune7 in his response to Mustali at 95 illustrates the significance of the point I am trying to make.

    Tribune writes, “The smallest chromosome is that of the Candidatus Carsonella ruddii, a bacteria, at 159,662 base pairs. For the four bases of DNA to arrange themselves by chance into a specific sequence of 159,662 base pairs is far, far beyond the UPB. I’d give you a number but my calculator doesn’t go that high.

    Now, you might want to challenge the specificity saying the structure would work adequately if …
    So you are going to resort to saying there must be an undiscovered necessity that causes the chemicals to self-organize in such a fashion.”

    Tribune’s calculation is based on the “pure chance hypothesis.” It is just a simple combinatoric calculation that assumes that each and every part simultaneously, and as a consequence of no causal connection, occurred at the right place and time in order to make the chromosome in question.

    No one believes that this is how the chromosome came to be, so I’m not sure what the value is of providing the calculation that it did arise by pure chance. Everyone, design advocate or design opponent of design agnostic, agrees that the chromosome did not arise by pure chance. As far as I am concerned, that issue is settled.

    But that is where the issue of how things do arise via natural processes comes into play. Tribune uses a common phrase when he writes, “So you are going to resort to saying there must be an undiscovered necessity that causes the chemicals to self-organize in such a fashion.”

    Well, no, the only alternative to pure chance is not “an undiscovered necessity.” Rather, as we look around us at what we do know about the world, we see that the basic laws of physics and chemistry cause all sorts of things to happen through the complexities of their interactions over time. Look at something like the layers of different types of rocks in the Grand Canyon, for instance. They reflect both a great deal of basic physics and chemistry taking place over time in a highly contingent fashion. There is no one “law” that says that particular pattern of those particular kinds of things must necessarily exist: they are the consequence of many long chains of causal and contingent connections.

    I am not a scientist and I know little about origin of life research, and the job of trying to understand how certain things happened billions of years ago under circumstances that no longer exist seems mind-bogglingly difficult to me: I’m amazed that we know as much as we do about that long ago in the past. I would be (will be, perhaps) very surprised if we ever have tremendously solid knowledge about the origin of life.
    But I do feel that it is correct to say, and this is my main point, that a calculation that such things could not have happened by pure chance does not imply that they couldn’t have occurred via natural processes.

    Interestingly, tribune7 in his response to Mustali at 95 illustrates the significance of the point I am trying to make.

    Tribune writes, “The smallest chromosome is that of the Candidatus Carsonella ruddii, a bacteria, at 159,662 base pairs. For the four bases of DNA to arrange themselves by chance into a specific sequence of 159,662 base pairs is far, far beyond the UPB. I’d give you a number but my calculator doesn’t go that high.

    Now, you might want to challenge the specificity saying the structure would work adequately if …
    So you are going to resort to saying there must be an undiscovered necessity that causes the chemicals to self-organize in such a fashion.

    This is basically resorting to faith to rebut Dembski’s science.

    Now, you might go out and do the hard work of finding and demonstrating such a necessity but that is much different than yapping about how it is contingent on us to show that one does not exist.”

    Tribune’s calculation is based on the “pure chance hypothesis.” It is just a simple combinatoric calculation that assumes that each and every part simultaneously, and as a consequence of no causal connection, occurred at the right place and time in order to make the chromosome in question.

    No one believes that this is how the chromosome came to be, so I’m not sure what the value is of providing the calculation that it did arise by pure chance. Everyone, design advocate or design opponent of design agnostic, agrees that the chromosome did not arise by pure chance. As far as I am concerned, that issue is settled.

    But that is where the issue of how things do arise via natural processes comes into play. Tribune uses a common phrase when he writes, “So you are going to resort to saying there must be an undiscovered necessity that causes the chemicals to self-organize in such a fashion.”
    Well, no, the only alternative to pure chance is not “an undiscovered necessity.” Rather, as we look around us at what we do know about the world, we see that the basic laws of physics and chemistry cause all sorts of things to happen through the complexities of their interactions over time. Look at something like the layers of different types of rocks in the Grand Canyon, for instance. They reflect both a great deal of basic physics and chemistry taking place over time in a highly contingent fashion. There is no one “law” that says that particular pattern of those particular kinds of things must necessarily exist: they are the consequence of many long chains of causal and contingent connections.

    I am not a scientist and I know little about origin of life research, and the job of trying to understand how certain things happened billions of years ago under circumstances that no longer exist seems mind-bogglingly difficult to me: I’m amazed that we know as much as we do about that long ago in the past. I would be (will be, perhaps) very surprised if we ever have tremendously solid knowledge about the origin of life.

    But I do feel that it is correct to say, and this is my main point, that a calculation that such things could not have happened by pure chance does not imply that they couldn’t have occurred via natural processes.

  99. Ouch – I am sorry about the formatting of the previous post. Scratch that – I goofed somehow. Here is the correct clean copy post:

    Interestingly, tribune7 in his response to Mustali at 95 illustrates the significance of the point I am trying to make.

    Tribune writes, “The smallest chromosome is that of the Candidatus Carsonella ruddii, a bacteria, at 159,662 base pairs. For the four bases of DNA to arrange themselves by chance into a specific sequence of 159,662 base pairs is far, far beyond the UPB. I’d give you a number but my calculator doesn’t go that high.

    Now, you might want to challenge the specificity saying the structure would work adequately if …

    So you are going to resort to saying there must be an undiscovered necessity that causes the chemicals to self-organize in such a fashion.”

    Tribune’s calculation is based on the “pure chance hypothesis.” It is just a simple combinatoric calculation that assumes that each and every part simultaneously, and as a consequence of no causal connection, occurred at the right place and time in order to make the chromosome in question.

    No one believes that this is how the chromosome came to be, so I’m not sure what the value is of providing the calculation that it did arise by pure chance. Everyone, design advocate or design opponent of design agnostic, agrees that the chromosome did not arise by pure chance. As far as I am concerned, that issue is settled.

    But that is where the issue of how things do arise via natural processes comes into play. Tribune uses a common phrase when he writes, “So you are going to resort to saying there must be an undiscovered necessity that causes the chemicals to self-organize in such a fashion.”

    Well, no, the only alternative to pure chance is not “an undiscovered necessity.” Rather, as we look around us at what we do know about the world, we see that the basic laws of physics and chemistry cause all sorts of things to happen through the complexities of their interactions over time. Look at something like the layers of different types of rocks in the Grand Canyon, for instance. They reflect both a great deal of basic physics and chemistry taking place over time in a highly contingent fashion. There is no one “law” that says that particular pattern of those particular kinds of things must necessarily exist: they are the consequence of many long chains of causal and contingent connections.

    I am not a scientist and I know little about origin of life research, and the job of trying to understand how certain things happened billions of years ago under circumstances that no longer exist seems mind-bogglingly difficult to me: I’m amazed that we know as much as we do about that long ago in the past. I would be (will be, perhaps) very surprised if we ever have tremendously solid knowledge about the origin of life.

    But I do feel that it is correct to say, and this is my main point, that a calculation that such things could not have happened by pure chance does not imply that they couldn’t have occurred via natural processes.

  100. Mustela — then you are failing to take into account known evolutionary mechanisms.

    And what were those know evolutionary mechanisms again?

  101. Tribune’s calculation is based on the “pure chance hypothesis,”

    No, aleta, it also includes specificity.

    that a calculation that such things could not have happened by pure chance does not imply that they couldn’t have occurred via natural processes.

    Which are unknown. IOW, your rebuttal is basically design could not have happened. Why do you think that?

  102. 102

    tribune7 at 100 and 101,

    And what were those know evolutionary mechanisms again?

    See Allen MacNeill’s blog post, referenced previously, for some examples.

    “Tribune’s calculation is based on the ‘pure chance hypothesis,’”

    No, aleta, it also includes specificity.

    No, you never described that part of the calculation.

    I’m genuinely interested in learning enough about CSI to be able to calculate it, but you are giving me the impression that you’re not interested in actually showing me how to do so. Back at 5 you stated:

    What ID says is that things that are designed have unique characteristics; these characteristics are quantifiable; and because these characteristics are quantifiable some things can conclusively be shown to have been designed.

    At 24 you stated that:

    CSI is certainly a respectable attempt to quantify those characteristics.

    So, you claim that designed artifacts have unique characteristics, that these characteristics can be quantified, and that CSI is a mechanism for doing so. The only way I, personally, would make such strongly stated assertions would be if I could readily demonstrate their veracity.

    Please demonstrate how to measure a characteristic of a biological system or component in order to determine whether or not it is designed. I’d be delighted if you showed how to measure CSI, but any “quantifiable” and “unique” characteristic will do.

  103. Aleta: “Tribune’s calculation is based on the “pure chance hypothesis,””

    Tribune: “No, aleta, it also includes specificity.”

    I don’t think specificity has anything do with the calculation itself – the calculation is just the probability that the base pairs would be exactly in the order that they are. Specificity is used in the design inference, but that is separate from just calculating the probability based on the pure chance hypotheis.

    Aleta: “that a calculation that such things could not have happened by pure chance does not imply that they couldn’t have occurred via natural processes.”

    Tribune: “Which are unknown. IOW, your rebuttal is basically design could not have happened. Why do you think that?”

    No, I have not said anything about whether design could or could not have happened. I am making a more limited point: irrespective of the state of our knowledge about how something might have arisen, a calculation that it arose by pure chance is irrelevant, because that is not the way natural processes work.

    I am arguing that you can’t jump conclusively to a design inference just because a pure chance hypothesis is ruled out (irrespective of the specificity issue.) This doesn’t mean that design might not have happened, but it does mean we may need to stay in a state of not knowing unless and until more positive evidence comes about.

  104. Aleta,

    Let me probe your mind a little. If I had a scrabble game, and I shook the box with the letters, and when I set it down the letters formed a sentence in english. Was that chance or law or both? How do you calculate it?

  105. Alerta:

    I am arguing that you can’t jump conclusively to a design inference just because a pure chance hypothesis is ruled out (irrespective of the specificity issue.)

    BINGO!!!

    If one follows the process set forth in the explanatory filter, to reach a design inference it is NOT enough to eliminate chance and necessity (and their interactions).

    Once those have been eliminated a specification must be met- even if that is as simple as “it looks designed”.

  106. Weasel Man:

    So, you claim that designed artifacts have unique characteristics, that these characteristics can be quantified, and that CSI is a mechanism for doing so.

    Do you think that archaeologists and forensic scientists just flip a coin to determine design or not?

    Take any biological system- the bacterial flagellum for example.

    Find out what it takes- genetically- to make one- each nucleotide would be two bits (not 25 cents).

    Then to refute the design inference for that all you would have to do is demonstrate that blind, undirected processes can account for it.

    If they can then you eliminate the requirement for a designer and falsify the design inference.

  107. Mustela Nivalis — See Allen MacNeill’s blog post, referenced previously, for some examples.

    Referenced previously and addressed previously, see Post 54.

    Which as a nice guy I will repeat:

    Two points (regarding MacNeill’s mechanisms):

    1. Those mechanisms are ultimately effects of chance according to Darwinism but that doesn’t really matter because . . .

    2. All those mechanisms depend on the pre-existence of chromosomes.

    So it seems that chromosome stands as example of a biological entity exhibiting CSI since it has complex specificity and the probability of it occurring by chance is greater than 1 in 10^150.

  108. Aleta– Specificity is used in the design inference, but that is separate from just calculating the probability based on the pure chance hypotheis.

    Not quite. For instance I am stipulating the existence of the bases, the backbone chain, that the required chemical bonding will happen etc.

    What I’m calculating the probability for is whether the bases can self-organize into the necessary information for the smallest known genome to function. And remember, this genome belongs to an endosymbiotic organism.

    And don’t discount the need for specificity in making my point. For instance, the odds of one particular snowflake falling on one particular square inch of Alaska at a particular instant would be beyond the UPB but it happens all the time.

    But suppose if one should shout out before hand when and where that particular snowflake should fall, would you attribute that to chance?

    Or suppose, after one particular snowfall, the snow spelled out the words “ID Rocks”. Would that make you go hmmmm?

    That would be more akin to the chromosome.

  109. To Collin at 104:

    Hi Collin.

    This is really just the same situation as the base pairs in a chromosome situation in that it assumes that all the sub-events (each letter showing up in a particular position in a string of letters) happen simultaneously with and independently of each other. While the shaking of the letters follows the laws of physics, the relationship between each letter, and any relationship this might have with the English langauge, is a matter of chance. (Actually, since the scrabble set has the number of tiles for each letter in approximate proportion to their use in English, this is weighted a bit towards English words occurring, but that doesn’t change the basic situation.)

    And since this is just another example of “pure chance”, my response is the same as before – this doesn’t help us any in thinking about what goes on in the real world because that’s not how real world events happen. Real world events don’t happen by having a bunch of completely independents things just coincidentally happen together at the same time. Real world events happen by having various things in causal relationships with both prior states and local neighbors in space interacting with each other. This is not a pure chance situation.

    The “pure chance” situation (be it scrabble tiles or dice or base pairs) is not an accurate model of the world, and therefore it can’t be used to argue about the world.

  110. 110

    tribune7 at 107,

    I’ll ask one more time before giving up, just in case:

    Please demonstrate how to measure a characteristic of a biological system or component in order to determine whether or not it is designed. I’d be delighted if you showed how to measure CSI, but any quantifiable characteristic that uniquely identifies design will do.

    If you can’t, please just say so.

  111. Mustela Nivalis — So, you claim that designed artifacts have unique characteristics, that these characteristics can be quantified, and that CSI is a mechanism for doing so. The only way I, personally, would make such strongly stated assertions would be if I could readily demonstrate their veracity.

    LOLOL. I missed this one.

    Maybe your primary concern should be reading comprehension rather than trying to understand CSI.

    For instance in post 5 I did not “claim that designed artifacts have unique characteristics,” etc.

    What I said was “ID says is that things that are designed have unique characteristics;” etc.

    A significant difference especially since the post was made in response to a mischaracterization of ID.

    But let’s consider these tenets: are you saying that things that are designed don’t have unique characteristics?

  112. Mustela Nivalis –Please demonstrate how to measure a characteristic of a biological system or component in order to determine whether or not it is designed.

    See posts 95 & 107 or 54 which address your concerns about not accounting for “known evolutionary mechanisms”

  113. 113

    tribune7 at 110,

    For instance in post 5 I did not “claim that designed artifacts have unique characteristics,” etc.

    What I said was “ID says is that things that are designed have unique characteristics;” etc.

    A significant difference especially since the post was made in response to a mischaracterization of ID.

    Fair enough. Do you not believe in the ID position?

    But let’s consider these tenets: are you saying that things that are designed don’t have unique characteristics?

    I’m not the one claiming there is or isn’t. I’ve been trying to get someone to clearly define such a characteristic so that it can be measured. Then we can see if it exists or not.

    CSI is supposed to be one such characteristic, but no one has yet provided an example of how to calculate it for a real biological system. I’m open to considering other measurements if you prefer.

  114. johnnyb,

    As an aside, I took some time to read a little bit of your work, and I think it’s among the best I’ve seen from the ID or Creationism position. I regard you, along with others like Atom and vjtorley, as a credit to your side of the debate.

    Your point regarding standard mutational theory is well taken. As a measure of how far somatic hypermutation deviates from the “mutation is random with respect to fitness” generalization, active info seems appropriate. Your example is a good one, and I stand corrected.

    With regards to other points, some measures (temperature, length, etc.) require no modeling. If we were to define those measures operationally, we could do so in terms of physical systems rather than mathematical abstractions.

    I think that active info is not such a measure. Given a search space, a subset of that space designated as the target, and a method for selecting points in the space, active info is unambiguous. But if we need to impose the space/target/method model on a given system, our choice of how to do so may depend on what question we’re trying to answer. For example, the question of how far somatic hypermutation deviates from the “mutation is random with respect to fitness” generalization yields a different model than the question of whether mutations are uniformly random across the 600-base variable region.

    Thank you for a good discussion and for showing useful application of the active info concept.

  115. Fair enough. Do you not believe in the ID position?

    Firstly, I believe ID is a worthy attempt describe nature.

    To get to the specifics:

    Regarding Tenet 1: I do believe design has unique characteristics, that this is obvious and it should be considered axiomatic

    Regarding Tenet 2: I believe these characteristics are quantifiable and that, since Tenet 1 should be held as axiomatically true, to say otherwise is rather anti-science. Now, as I think I said in a later post, whether ID succeeds in this quantification is TBD, but it certainly is an honest attempt.

    Regarding Tenet 3: I believe that because these characteristics are quantifiable some things can conclusively be shown to have been designed. Again whether IDs methods have successfully done so is TBD.

    And to really understand CSI, rather than challenging me, check out what Dembski says about it himself at DesignInference.Com or even shell out some money for one of his books.

  116. Mustela, I’d love to get into this again but at the moment I’m too busy. Wasn’t it you that I already showed how to calculate CSI of the protein Titin?

    http://www.uncommondescent.com.....ent-341828

    So, if that was indeed you that I was responding to, why are you stating that “no one has yet provided an example of how to calculate it for a real biological system?”

    Or are you just being specific with the word “system.” In that case, since biological systems are composed of proteins, then utilize the same calculation for all proteins in the system, do some research on the specificity of the system — ratio of functional arrangements of proteins of that probability (information storage size) to non-functional — and you are pretty much good to go.

    Hopefully I can get back to you and we can work out the CSI of a small biological system together after this weekend.

    BTW, your last comment at the link I’ve included above within this comment betrays your lack of understanding of the reality of the “fine tuning problem” in physics that many physicist have provided published papers to address. The question is: “out of all the mathematically possible values that could describe our laws, how are they in a “knife’s edge” balance (especially the cosmological constant) in relation to each other in order for life to exist, develop, and evolve?

    CSI doesn’t “take into consideration” that our universe is fine tuned for life, since it is indeed the type of calculation that *shows us* that our universe is fine tuned for the evolution of life. CSI is the evidence of evolution (barring direct intervention) and evolution is the evidence of previous intelligence.

  117. I took a quick look at CJYman’s post and it’s more of the same simple combinatorics. None of these calculations take into account either a series of events leading to an end result or possible inter-dependencies between components, so, as I said above, I don’t think they accurately model the real world.

  118. Mustela Nivalis @ 89:

    That’s a red herring. I’m trying to understand the objective, positive evidence for ID.

    If you believe that natural selection can imitate design, and if this belief is an objective belief, then you must have objective evidence for design.

    So why are you asking for something you already have or know?

    Of course, it’s possible that you don’t believe natural selection can imitate design. If this is so, why not just say so?

    It’s also possible that you do believe natural selection can imitate design, but have no objective reason for believing it. If this is so, why not just say admit it?

  119. None of these calculations take into account either a series of events leading to an end result or possible inter-dependencies between components,

    What are those series of events and inter-dependencies, Aleta?

  120. I don’t know.

    But the argument doesn’t rise or fall on my lack of knowledge, or humankind’s lack, for that matter.

    A calculation that doesn’t take into account the basic structure of how things happen in the world, and just assumes pure chance, is not an accurate model of the world. That fact is true irrespective of whether someone else does or does not have a better model.

  121. Aleta, you are appealing to unseen forces to reject design.

    Pure chance could not have created the chromosome.

    It was either an unknown necessity of nature or design. Why do you reject design?

  122. I’m afraid you are not understanding my point. I don’t need for you to agree with my argument, but I would like you to understand my position.
    First, we agree that pure chance could not have created the chromosome. That is not an issue between us.
    But I disagree when you say that I am appealing to “unseen forces” and I disagree with the dichotomy that “It was either an unknown necessity of nature or design.”

    I am saying that rejecting the pure chance hypothesis does not allow one to conclude design because things in the world never happen by pure chance anyway. Most things happen by known forces (not unknown ones) interacting in ways that, in part because of the contingent aspect of the history of events, lead to novel results. There doesn’t have to be a “necessity” of nature for nature to produce something. The interplay of natural forces along intersecting causal chains of events is creative, and produces things which are contingent, not necessary – that is, they might not have happened, but they did.

    This fact about how things work needs to be recognized. An argument that doesn’t take this into account will necessarily be faulty, I think.

    You ask, “Why do you reject design?”

    I haven’t said whether I reject design or not. What I have said is that the argument that something couldn’t have arisen by pure chance is not, in any way, a positive argument for design.

    Here is a somewhat flippant example, using an analogy commonly used by ID advocates.

    Suppose a house burns down and the arson inspector shows up. Imagine him saying, “Hmmm. The probability of all the particles in this house suddenly arranging themselves so as to cause the house to spontaneously completely burn into flames is impossibly low. Therefore I conclude arson.”

    This is what the arguments that I’m reading here are like: Creation by pure chance is impossible, therefore ID.

    The argument is faulty. I reject this argument. Give me better evidence for design if you want to be convincing, but it would be useful, perhaps, for you to accurately understand what it is I reject, and why.

    By the way, I appreciate the civil and thoughtful discussion.

  123. Alerta,

    First it is a fire inspector that shows up and may or may not determine arson.

    He/ she does that by going over the evidence.

    This is what the arguments that I’m reading here are like: Creation by pure chance is impossible, therefore ID.

    As I had told you before that is not how it goes.

    The explanatory filter mandates that not only chance and necessity be eliminated but also a specification be met.

    As for chromosomes- well they are more than just base pairs, you guys realize that, right?

  124. Mustela Nivalis:

    I’ll ask one more time before giving up,

    You gave up before you started posting here.

    Guys don’t waste your time with weasel man.

    He won’t be satisfied until you introduce him to the designers.

    R0b, Alerta, Zachriel, MacNeill, the NCSE, the NAS- they are all the same.

    They can’t support their position- all they have to do to falsify ID- so they have to pick on something until it gets infected and oozes puss.

  125. Joseph writes, “First it is a fire inspector that shows up and may or may not determine arson.”

    Sorry – I wrote arson inspector – my bad.

    Joseph writes, “The explanatory filter mandates that not only chance and necessity be eliminated but also a specification be met.”

    I understand the specification part, Joseph, but it’s not relevant to my argument. My argument is that “necessity” has not been eliminated. I am also arguing that “necessity” is not being properly understood.

    P.S. – it’s Aleta, not Alerta, although I am alert. :)

  126. Oops – after reading Joseph’s post at 123 I see that he is not someone I want to discuss things with. I’m committed to civil and thoughtful discourse and I see that is not something I can expect from Joseph.

  127. Hello Aleta,

    You stated, regarding CSI:
    “None of these calculations take into account either a series of events leading to an end result or possible inter-dependencies between components, so, as I said above, I don’t think they accurately model the real world.”

    The calculation most definitely takes into account a series of events. It covers all chance events within available probabilistic resources, and if the calculation > 1 we have evidence that the series of events preceding the event in question are not random, but contain some element of either law and/or something else.

    Chance as an explanation: an event of leaves blowing around in your front yard. There is no independent pattern to formulate the event of where the leaves are positioned relative to each other. Thus, there is no correlation. Chance/randomness is a lack of correlation. Furthermore, the position of the leaves and their motion does not result from the material properties of the leaves themselves. There is no mathematical pattern to describe the position of the leaves in relation to each other. We can say that the event of the leaves blowing around in your yard is random, the pattern of leaves is arrived at by chance. Of course, there are laws “blowing around” in the background, indirectly affecting the leaves. This is why I don’t see how “pure chance” can exist apart from law. However, the pattern of leaves we say does not show a lawful pattern and is thus “random” — resulting by chance.

    Here is a more in-depth explanation of the difference between law and organization such as CSI:

    http://www.uncommondescent.com.....ent-337588

    As to the “inter-dependence” between components, are you referring to the forces that the components exert upon each other? If so, you are referring to the lawful forces of nature and it seems to me that CSI does not take law into consideration. A lawful event would be specified through compression. That is what a law is — a mathematical description/algorithm/compression of regular events. That is why the explanatory filter is necessary.

    Think of ruling out “law” this way — can this essay be defined by the laws of the components utilized (by either mathematical description of regularity and/or regularity resulting from the material/measurable properties of the components)?

    Basically it comes down to the difference between the following types of patterns, no matter the events preceding them …

    ajdsjdhhfieperi — best explained by chance (no correlation)

    aaaaaaaaaaaaaaa or agfdagfdagfdagfd — best explained by chance + law (compressible)

    “Can you understand this” — best explained by chance + law + intelligence (correlated/specified and improbable/complex)

    In fact, an evolutionary algorithm is the best example of chance, law, and intelligence working together.

    If you disagree with utilizing CSI as a hallmark of intelligence, then please just provide evidence of CSI produced from a random set of laws (laws + chance) absent any intelligent “fine tuning” for future results. Random.org could come in helpful for such an experiment. Will such a set up produce evolution and CSI?

  128. Also Aleta,

    By “necessity” do you mean “determined” or “necessitated by material properties?”

  129. Aleta — I am saying that rejecting the pure chance hypothesis does not allow one to conclude design

    And you would be right. Go re-read my post 108 and see if our position becomes any clearer.

  130. CJYman — nicely done regarding 126.

  131. I’m committed to civil and thoughtful discourse and I see that is not something I can expect from Joseph.

    It’s not something you can expect from anyone, so why pick on Joseph.

    He can no more expect it from you than you can expect it from him, though, to be perfectly frank, his view permits him to expect rational discourse from others, while your view provides no grounds whatever for such an expectation.

    iow, Joseph is at least being consistent, while you are not.

    Tell me, on your view of things, what is the basis for rational discourse?

  132. Aleta:

    My argument is that “necessity” has not been eliminated.

    Only someone who requires absolute proof would say something like that.

    There is nothing to discuss with someone like that.

    I am also arguing that “necessity” is not being properly understood.

    Hawkings says that the laws that govern nature “Just are (the way they are)” Briefer History of Time”- what else is there to understand? :)

    Thoughtful discourse my ….

  133. Aleta@122:

    First, we agree that pure chance could not have created the chromosome. That is not an issue between us.

    1. Why not?
    2. What else is there?

    I haven’t said whether I reject design or not.

    So why not say? Why would it be unreasonable for someone to think that you do?

    If you don’t reject design, where do you see it, and how do you recognise it?

  134. VMARTIN:

    Scherer departed from Discovery Institute and his career in Germany seems quite impressive. Anyway he follows ID movement with great sympathy as he wrote in an interview 2 year ago.

    Prof. Scherer’s position is not really clear. Following his interviews I get the impression that he is floating with the tide and that his statements depend on the audience he is addressing: On the one hand he believes that the bible is literally true (Biblische Schöpfungslehre). On the other hand he says that the Bible interpretation of “US creationists” (his words) is wrong although he published young earth articles (e.g.: “To much coal for a young earth?”). On his “Wort und Wissen” web pages you will also find articles about the size of Noah’s arch (though not authored by Prof. Scherer). At the same time he dismisses ID (he stated “ID is not science and shouldn’t be taught in schools”), creationism as well as evolution theory. Thus, one has to wonder what his “Biblische Schöpfungslehre” actually is about.

    BTW, I always thought VMartin is just another blogging identity of Prof. Davison.

  135. I’ve been reading the FAQ, and I’m not sure of the relationship between FSCI and CSI. Are there any further resources available (google suggests it’s an oil company) or could somebody explain the relationship between FSCI and CSI with an example?

    It’s odd, from what I understand of FSCI from the FQA, that it’s not been mentioned on this thread in conjunction with CSI.

    So, since in the cases of known origin such are invariably the result of design, it is confidently but provisionally inferred that FSCI is a reliable sign of intelligent design.

    This is very interesting stuff indeed! Is there a list of objects and their values for FSCI available?

    What units is FSCI measured in? I was not able to determine that from the FAQ.

  136. to Tribune at 128

    You write, “Aleta — I am saying that rejecting the pure chance hypothesis does not allow one to conclude design. And you would be right. Go re-read my post 108 and see if our position becomes any clearer.”

    I understand the role of specification in ID theory, but I’ve said it’s not relevant to my point.

    I can rewite the above sentence this way, if you like: “I am saying that rejecting the pure chance hypothesis, even if the configuration in question is specified, does not allow one to conclude design.”

    The reason is that no one thinks that pure things come into existence anyway, so eliminating the pure chance hypothesis adds nothing to what we already know. Even if the pure chance hypothesis is eliminated, the hypothesis that some series of contingent natural events are the cause of the thing in question has not been eliminated, so jumping to the conclusion of design is not warranted.

    And, to repeat myself, eliminating the “natural processes” hypothesis is not just simply a matter of claiming there is no known law that would produce the thing in question, or that some “unknown force” needs to be invoked to make it necessary, which are the ideas that have been offered in this discussion. The world is more complex than that, and until ID theorists take a stab at trying to calculate probabilities based on a realistic model of how the world works, arguments based on probablities will be faulty.

  137. Edit:

    The confused sentence above “The reason is that no one thinks that pure things come into existence anyway, so eliminating the pure chance hypothesis adds nothing to what we already know.”

    should read

    “The reason is that no one thinks that things come into existence through pure chance anyway, so eliminating the pure chance hypothesis adds nothing to what we already know.

  138. Chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, is at the very root of the stupendous edifice of creation.-Nobel Prize-winning chemist Jacques Monod

  139. Aleta,

    Scientists have to work with the knowledge currently available.

    They cannot and do not wait for what the future may or may not uncover.

    All scientific inferences may indeed by faulty but that is the nature of the beast.

  140. Joseph,
    I disagree with that. IOW it’s never been shown that chance is even capable of creating the transformations required to create complex life forms. For example, is there genetic any data which would demonstrate that the transformations required, if cetaceans evolved from land mammals, are even possible?
    IOW is there any way to test te premise (that cetaceans evolved from land mammals) without first assuming it?

    Can you provide that proof?

  141. Joseph

    Scientists have to work with the knowledge currently available.

    Given that, what is better supported by the available evidence? ID or your “chance” theory?
    There isn’t any genetic gata which we could use to test that premise of descent with modification can lead to the diversity of life from some unknown population(s) of single-celled organisms.

    Yet the “theory” of evolution is considered scientific.

  142. 142

    tribune7 at 115,

    Regarding Tenet 1: I do believe design has unique characteristics, that this is obvious and it should be considered axiomatic

    You’ve just attempted to assume away the part of your claim that is most difficult to support. What, exactly, are these unique characteristics? How, exactly, can they be measured?

  143. 143

    CJYman at 116,

    Mustela, I’d love to get into this again but at the moment I’m too busy.

    Nice to see you posting again. I look forward to discussing this with you when you have the time.

    Wasn’t it you that I already showed how to calculate CSI of the protein Titin?

    Well, you claimed to compute the CSI of titin, but you had to leave the thread before you explained how to objectively determine the specification. Your calculation also boiled down to little more the naive calculation of 2 to the power of the length of the genome. Without the specification and without taking into consideration known physics, chemistry, and evolutionary mechanisms, your example didn’t actually show how to calculate CSI.

    I’d be very interested in hearing your response to the issues raised in that thread.

  144. I do believe design has unique characteristics, that this is obvious and it should be considered axiomatic

    Can you give an example of a biological object that was

    a) designed
    b) not designed

    ?

    If you can, can you explain how that was determined? I’m aware of DBB and the bac. flag example. Do you have another, or is it just the one?

    Also, for each example of a designed and a not-designed object could you state the value for the CSI or FSCI (ideally both) in each of those objects?

    Or, failing all that, can you tell me the CSI or FSCI for anything at all, biological or not?

    Let’s bring out some facts to base this on. Maths is a good start.

    What units is FSCI measured in?

  145. Aleta,

    What you call chance I would call merely further along the continuum of interconnectivity. I mean, when you go further back in time, the english language and scrabble have the same causes, dovetailing into the Big Bang. I don’t really see them as independent or dependent.

    If you were present at the Big Bang, and were to calculate the chance of a chromosome arising, it would be the same as shaking a boggle cube (and its boggle not scrabble, my bad).

    Listen, I think that if we follow your analysis then we take all the physical factors out of the chance category and put them in the law category (or some other category which seems to me to be an ill-defined category), including
    1. The earth being in the “goldilocks zone”
    2. Just enough oxygen in the atmosphere
    3. an RNA world

    etc etc etc.

    All of those physical law and events and factors being precisely in the right place at the right time to create a chromosome, is pure chance.

  146. h.pesoj-

    RotFLMAO-

    We have the weasel man Mustela Nivalis, and now h.pesoj, which, of course, is just my name spelled backwards.

    IOW we have TROLLS! :cool:

  147. Ooops, almost forgot-

    Don’t feed the TROLLS!

  148. h.pesoj — Can you give an example of a biological object that was designed . .

    That’s what the debate’s about isn’t it?

    Do you agree that design exists and is quantifiable?

  149. and now h.pesoj, which, of course, is just my name spelled backwards.

    LOL. Good catch Joseph.

  150. Tribune7

    Do you agree that design exists and is quantifiable?

    That it exists, of course. That it is quantifiable? Of course.

    That it has been quantified? No. Not yet. Perhaps never.

    Just give me the examples, and we’ll see then, won’t we?

  151. That it exists, of course. That it is quantifiable? Of course.

    OK, then. ID is an attempt to do so. You think it fails. Why?

  152. Tribune, I believe the issue that both Mustela and I are interested in is how ID advocates propose to measure the qualities (CSI, or whatver) that supposedly support the design inference.

    As far as I can tell the only such calculations that have been done are very simple ones involving the multiplication rule for independent events, and these, as I am arguing, are not an accurate model of how things in the world come to be.

    Later in the day, when I have more time, I’ll provide an example I’ve been thinking about to provide some more details.

  153. tribune7,

    OK, then. ID is an attempt to do so. You think it fails. Why?

    The first answer to that question is that you cannot provide the two examples I’m asking for in 140.

  154. I believe the issue that both Mustela and I are interested in is how ID advocates propose to measure the qualities (CSI, or whatver)

    Aleta, there is a very detailed explanation in the glossary, which might be exactly what you are looking for

  155. h.pesoj –The first answer to that question is that you cannot provide the two examples I’m asking for in 140.

    I’m respecting you enough not to treat you as stupid. There have been examples posted on this thread – chromosomes and proteins. Why do you think ID fails when it indicates them to be designed?

  156. h.pesoj

    For a biological item not designed, maybe a dead twig blown randomly to the ground — after it died and was on the ground.

    But whatever the DNA had coded for would be designed.

  157. I’m arguing that all the calculations that ID advocates provide to measure a quantity (CSI et al) that can be used to infer design are irrelevant because they do not model the real world accurately.

    Here’s an example to provide some more detail to explain what I mean.

    Throw 10 dice. What is the probability that they will be all sixes?

    Easy problem: (1/6) ^ 10 = 1 out of 60,000,000, approximately

    Harder problem: The ten dice are in a box which periodically jiggles hard enough to toss all the dice. However, the sides with a 1 on it are sticky, so if a dice comes up six, it sticks.

    Now the box jiggles five times. What is the probability that after five jiggles you have all sixes.

    This is more complicated. First, for any one throw you need to calculate the probability of getting no sixes, one six, two sixes, etc., so you have to use the binomial probability theorem. Then, for each subsequent throw you have a different number of dice being jiggled (ten if no sixes, 9 if one six,etc.), so you have both a continued use of the binomial probability theorem and a complex probability tree that branches ten times on the first throw and some varying numbers on each of the subsequent throws.

    This second situation is more like the real world: it has a sequence of events (it models the passage of time in a very simple way) and it has laws (the one side sticks) that add an element of direction and selection.

    At a vastly more complicated level, this is what ID advocates needs to be trying to do if they want to meaningingfully provide a probability calculation that might imply design. Such calculations need to take into account a sequence of steps over time and they need to take into account that various laws of physics and chemistry create changes along those series of steps that then change the types of changes that can further happen. Only by trying to do such will ID advocates being working towards an accurate mathematical model of the world.

    This is why Mustela and others are asking for a method – one that can be reliably used by any interested party, to measure the CSI of a biological entity. Until such a method is developed, shared, and tested by multiple sources, the idea of CSI will be unusable.

  158. 158

    tribune7 at 151,

    “I believe the issue that both Mustela and I are interested in is how ID advocates propose to measure the qualities (CSI, or whatver)”

    Actually, we need to start one step further, with my first question from 138:

    tribune7 at 115,

    “Regarding Tenet 1: I do believe design has unique characteristics, that this is obvious and it should be considered axiomatic”

    You’ve just attempted to assume away the part of your claim that is most difficult to support. What, exactly, are these unique characteristics?

    Once those are identified, we can get to the second question of how, exactly, they can be measured.

    Aleta, there is a very detailed explanation in the glossary, which might be exactly what you are looking for

    The glossary does not define CSI with sufficient rigor to apply it to a real biological system or component, nor does it provide references to worked examples of doing so.

    I’m very interested in your answers to my 138.

  159. Aleta, did you read the description of CSI in the glossery?

  160. Aleta:

    This is why Mustela and others are asking for a method – one that can be reliably used by any interested party, to measure the CSI of a biological entity.

    The method has been provided.

    For living organisms find the minimal genome required, count the nucleotides.

    Each nucleotide is equal to 2 bits.

    CSI is present if there 500 bits or more*.

    (* may be a little lower)

    For the bacterial flagellum- same thing.

    Find the sequences responsible for its construction and count the bits.

  161. Mustela, sorry I missed 138.

    Regarding Tenet 1: I do believe design has unique characteristics, that this is obvious and it should be considered axiomatic . . .You’ve just attempted to assume away the part of your claim that is most difficult to support. What, exactly, are these unique characteristics? How, exactly, can they be measured?,

    It isn’t assuming away anything. It’s stating a starting principle i.e. Design has unique characteristics. Once we agree upon that we can start discussing what those characteristics might be.

    Turn it around: Design does not have unique characteristics. Can you advocate for that position?

  162. To support my last comment I offer:

    Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the same sense required by the complexity-specification criterion (see sections 1.3 and 2.5). The specification of organisms can be crashed out in any number of ways. Arno Wouters cashes it out globally in terms of the viability of whole organisms. Michael Behe cashes it out in terms of minimal function of biochemical systems.- Wm. Dembski page 148 of NFL

    In the preceding and proceeding paragraphs William Dembski makes it clear that biological specification is CSI- complex specified information.

    In the paper “The origin of biological information and the higher taxonomic categories”, Stephen C. Meyer wrote:

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

    In order to be a candidate for natural selection a system must have minimal function: the ability to accomplish a task in physically realistic circumstances.- M. Behe page 45 of “Darwin’s Black Box”

    He goes on to say:

    Irreducibly complex systems are nasty roadblocks for Darwinian evolution; the need for minimal function greatly exacerbates the dilemma. – page 46

  163. Mustela — The glossary does not define CSI with sufficient rigor to apply it to a real biological system or component,

    Rigor is subjective but for an application to a biological system or component look under EF Explanatory Filter.

  164. Tribune7

    Rigor is subjective but for an application to a biological system or component look under EF Explanatory Filter.

    Would it be possible for you to run us through an example of the usage of the EF?

    If not, what artifacts has the EF determined are designed? And not designed?

    Is there a list?

    There must be more then 1 example available. Or will I have to “buy the book” (just tell me the page number as it goes)?

    Is there a difference in how you apply the EF to a “biological system” and a “component”? What is it?

    I’ve looked at the entry in the FAQ. I saw no list.

  165. Joseph

    To support my last comment I offer:

    Offer all the quotes you want. The fact that you can’t provide something as simple as the value for the CSI/FSCI in *anything at all* kind of undermines your argument. Or a list of biological items ordered by complexity.

    And quoting books is fine, but don’t you have any papers or articles from peer reviewed sources to quote?

  166. h.pesoj — Would it be possible for you to run us through an example of the usage of the EF?

    I guess, but it would be easier for you to scroll to the top of the page, click on the link and read it yourself.

  167. I guess, but it would be easier for you to scroll to the top of the page, click on the link and read it yourself.

    I see no such link to an example of the EF in action. And I take it then that you cannot provide a list of items that have passed/been rejected by the EF.

    Tell me, given that no biologist would suggest that a modern chromosome came together by chance why do you continue to claim that the probability of it happening by chance is relevant to anything at all?

    The smallest chromosome is that of the Candidatus Carsonella ruddii, a bacteria, at 159,662 base pairs. For the four bases of DNA to arrange themselves by chance into a specific sequence of 159,662 base pairs is far, far beyond the UPB. I’d give you a number but my calculator doesn’t go that high.

    Tell me, for this to be relevant you have to know what is happening when “arrange themselves by chance” is happening? Is it a machine trying each combination one by one?

    When you talk about chromosomes coming together by chance what process do you imagine is happening? A big mixing vat with all the parts sloshing around? A line of chemicals on a belt, moving step by step?

    What is happening?

  168. Tribune at 156: “Aleta, did you read the description of CSI in the glossery?”

    Yes. It tells how to compute CSI given that you know a probability, but it does not tell how to compute the probability upon which the CSI is based.

  169. P.S I note that in both the glossary article on CSI and on the EF, the only examples are of the same kind as I have been objecting to, so there is nothing new for this discussion in those two articles.

  170. 170

    tribune7 at 158,

    Mustela, sorry I missed 138.

    No problem at all — this thread is getting busy.

    Regarding Tenet 1: I do believe design has unique characteristics, that this is obvious and it should be considered axiomatic . . .”You’ve just attempted to assume away the part of your claim that is most difficult to support. What, exactly, are these unique characteristics? How, exactly, can they be measured?”

    It isn’t assuming away anything. It’s stating a starting principle i.e. Design has unique characteristics.

    That’s not a principle, it’s an assertion about an observation.

    Once we agree upon that we can start discussing what those characteristics might be.

    There’s no reason to assert it in the first place if you haven’t observed any characteristics that uniquely identify design.

    What, exactly, are the characteristics that you believe uniquely identify design?

  171. Aleta, It tells how to compute CSI given that you know a probability, but it does not tell how to compute the probability upon which the CSI is based.

    No, it tells you specifically how to compute the probability i.e. a given target zone in a search space, on a relevant chance hypothesis.

    CJYman summed it up well in Post 126.

  172. backwards me wrongly states:

    It’s amazing that for all the claims that are made for the EF and how it proves the “intelligent designer” exists

    The EF is not about “proof”.

    The EF is about an inference- an inference based on the evidence- all the evidence and the context- PLUS our current understanding on cause and effect.

    And as with ALL scientific inferences it can be either confirmed or falsified with future research/ knowledge.

    That possibility sure didn’t stop Einstein.

    The fact that you can’t provide something as simple as the value for the CSI/FSCI in *anything at all* kind of undermines your argument.

    Unfortunately for you I have done exactly that.

    I have also taken the time to tell others how to do it.

    I have done that in this very thread.

    And others have done so in various pro-ID writings.

    But anyway how do you think that archaeologists determine an artifact from a rock?

    Do you think they flip a coin?

    How about forensic scientists- do they flip a coin to determine whether or not a crime has been committed?

    Wise up trolls.

    Humans have tried and true design detection techniques- used daily.

    We have a good amount of experience/ observations of cause and effect.

    All your position has is the refusal to accept the design inference because you just refuse to understand ID.

    As I said in the end it doesn’t matter about CSI.

    All the trolls have to do is to actually start supporting their position and ID would fade away.

  173. h.pesoj — Tell me, given that no biologist would suggest that a modern chromosome came together by chance

    If they reject design it’s either chance or handwaving. What are the forces that biologists say cause the chromosome, modern or otherwise, to come together?

    Why do reject the possibility of design?

  174. BTW you want to know who should be using the EF?

    The very people who try to argue against ID.

    The explanatory filter (EF) is a process that can be used to reach an informed inference about an object or event in question.

    The EF mandates a rigorous investigation be conducted in an attempt to figure out how the object/ structure/ event in question came to be (see Science Asks Three Basic Questions, question 3).

    So who would use such a process? Mainly anyone and everyone attempting to debunk a design inference. This would also apply to anyone checking/ verifying a design inference.

    As I said in another opening post, Ghost Hunters use the EF.

    The EF is just a standard operating procedure used when conducting an investigation in which the cause is in doubt or needs to be verified.

  175. Mustela — Design has unique characteristics. . .That’s not a principle, it’s an assertion about an observation.

    It’s an assertion of a principle. Do you accept or reject the claim?

  176. Thank you to Mustela, Aleta, and h.pesoj for pointing out that all reported CSI calculations are based on a single null hypothesis, namely uniform chance. On the plus side, this makes CSI calculations tractable in at least two ways: 1. P(E|H) is straightforward to calculate, and 2. It’s easy to determine that the CINDE condition is met — that is, the specification is independent of the event. (Under a hypothesis of random chance, the event is independent of everything.)

    But on the negative side, the best that a uniform-chance-based calculation can accomplish is indicate that the hypothesis of uniform chance should be rejected. In the case of biological structures, nobody has proposed pure random chance as a hypothesis, so such calculations accomplish nothing.

    Dr. Dembski warns that in order for a design inference to get going, we must “know enough to determine all the relevant chance hypotheses” and “we must have a good grasp of what chance hypotheses would have been operating to produce the observed event”. Have we met these conditions when it comes to calculating the CSI in biological/chemical structures?

  177. Tribune says the glossary tells how to compute the probability upon which CSI is based when it says “a given target zone in a search space, on a relevant chance hypothesis.”

    Yes, but how do you do that? If you take into account the history of how a thing came into existence as opposed to just a simple look at its present configuration, how do you calculate the number of states required to compute the probability?

    I’ll also note that the quoted sentence refers to the “relevant chance hypothesis”, which makes me think that the only thing the glossary has in mind is exactly the kind of “pure chance” calculations that I am saying are not relevant because they do not model the real world.

    So I’m wondering why you or others are not responding to my point that if you want to have a realistic model with which to try and calculate probabilities, you have to take both the passage of time and the existence of natural processes by which states slowly change as they progress from a beginning state to an end state, such as I tried to explain with my dice example? Do you see anything reasonable in this point I am making?

  178. R0b — But on the negative side, the best that a uniform-chance-based calculation can accomplish is indicate that the hypothesis of uniform chance should be rejected.

    How can someone who believes in an undesigned universe reject uniform chance?

  179. Note: In the above two quotes by Dr. Dembski, “chance hypotheses” include all natural hypotheses, even those that are deterministic. Says Dembski, “Chance as I characterize it thus includes necessity, chance (as it is ordinarily used), and their combination.”

  180. R0b:

    Thank you to Mustela, Aleta, and h.pesoj for pointing out that all reported CSI calculations are based on a single null hypothesis, namely uniform chance.

    Yet that is false.

    Ya see in “No Free Luch”- the book that starts the talk about CSI and calculting- it states that chance and necessity are considered together.

  181. tribune7:

    How can someone who believes in an undesigned universe reject uniform chance?

    If the phenomenon in question is not statistically random, why would anyone *not* reject the hypothesis of uniform chance? Everybody rejects this hypothesis as an explanation for biological structures.

  182. Aleta — If you take into account the history of how a thing came into existence as opposed to just a simple look at its present configuration, how do you calculate the number of states required to compute the probability?

    You would attempt to determine the number of possible operations in our observed universe to serve as a reasonable upper limit on the number of search operations.

    And if someone should challenge you, say by claiming that there were circumstances that occurred that drastically cut the odds, you would ask what they were, be told and calculate accordingly.

    And if the person should be unable to tell you what those circumstances were but insist they occurred, you’d just have to shrug and respect that person’s faith that accidents reign supreme.

    But what can be measured i.e. science would be on your side.

  183. Aleta — Do you see anything reasonable in this point I am making?

    If I were insisting on making a claim of dogma, yes.

    But otherwise I just see you ignoring the claim, I’m making — namely design is a quite reasonable, maybe even the most reasonable, claim for how life came about.

  184. Note to Clive Hayden-

    Do not ban any other evo.

    Every time you do two or more others just jump in and muddy the waters even more.

    Banning evos is like fighting mythical monsters…

  185. Tribune says, “How can someone who believes in an undesigned universe reject uniform chance?”

    This remark takes me back to the comment Collin made many posts ago that got me interested in this discussion. The statement makes no sense to me, and I would genuienely like to understand what understandings Tribune has to say such a thing.

    First, I don’t think the topic here has been whether the universe is designed or not (that is a much larger question) – the much narrower question (to which I answer “no”) is whether the kind of calculations being offered can tells us anything about whether a particular thing is designed.

    Furthermore, surely Tribune doesn’t mean he thinks that everything happens by uniform chance? Apples fall down all the time, and there is no chance involved in that.

    Irrespective of whether the universe as a whole has been designed to have the nature it has, within this universe virtually all events happen in part because of lawful natural processes.

    So I am not rejecting uniform chance as an hypothesis that can apply to some situations – it certainly applies to throwing 10 dice, but I reject the hypothesis that that is relevant to the development of most events in the world.

    P.S.

    And in No Free Lunch, despite what Dembski says about chance and necessity working together, the example he uses is just another calculation based on a pure chance arrangement of components.

  186. R0b– If the phenomenon in question is not statistically random, why would anyone *not* reject the hypothesis of uniform chance?

    Because an undesigned universe would come from chance since the physics can’t precede the universe, and this of course would make the physical laws subordinate to chance which would mean we couldn’t ultimately trust the physical laws.

  187. Aleta, 185 is for you too, I guess.

  188. Hmm. I’m thinking this conversation might be winding down because it’s getting fairly repetitious.

    Tribune says, “But otherwise I just see you ignoring the claim, I’m making — namely design is a quite reasonable, maybe even the most reasonable, claim for how life came about.”

    I’m not ignoring your claim. I am arguing against your claim with quite a bit of specificity, giving reasons and examples. That is not ignoring.

    Your claim is that “design is a quite reasonable, maybe even the most reasonable, claim for how life came about.” My point is that the reasons you give for this claim are not convincing, and appear, for reasons I have gone to some length to explain, to be faulty.

    The heart of my argument, which I don’t believe you have addressed, is that real world events are much more complicated than the simple pure chance calculations that are offered by ID advocates. This is an argument against your claims – since I am clearly not ignoring your claim, would you like to respond to my point?

  189. And in response to 186, I’m not interested in taking this conversation to metaphysical discussions about the origin of the universe. We are talking about how we in this universe go about studying the universe.

    In fact, as I have alluded to, you have no idea whether I think the universe is designed or not, because I’m not interested in having that be part of the universe. I may be a theist, a deist, a Buddhist, a materialist, or even a front-loading IDist as mentioned in the opening post (remember the opening post?)

    My focus is narrow: the calculations being offered as support for the design inference are faulty. I have even stated what I think ID advocates should be doing to rectify this situation if they want the probability argument to have traction.

    So I have not been arguing against design: I have been arguing against a specific argument that purports to support design. There’s a significant difference between those two things.

  190. Aleta — The heart of my argument, which I don’t believe you have addressed, is that real world events are much more complicated than the simple pure chance

    Response 1 — You are asking for certainty and I’m not going to give it to you.

    Response 2 — Probability calculations, even simple ones, are a legitimate part of the search for design and you use them whether you care to admit it or not. If valuables are missing after every visit from Joe you will assume design based on probability calculations and respond accordingly.

    Response 3 — Your dismissal of ID is based on you being able to imagine situations in which it fails — which, btw, means it is potentially falsifiable and legitimate science by one common definition. This, no offense, is not much different than a Younger Earther rejecting an old Earth because science cannot conclusively show that radioactive decay was a constant a billion years ago.

    Last, but not least:

    Response 4 — If real world events are much more complicated than simple pure chance, they are designed.

  191. OK, I retire, but with some parting remarks.

    Response 1 — You are asking for certainty and I’m not going to give it to you.

    For the life of me I see nothing in what I’ve said as being asking for certainty.

    Response 4 — If real world events are much more complicated than simple pure chance, they are designed.

    As I’ve said. this remark makes no sense to me. Going back to earlier posts, this means lightning is designed, for instance – it means virtually everything in the universe is designed, in fact. That use of the word design is far broader than the definition commonly used by ID advocates.

    Response 3 — Your dismissal of ID is based on you being able to imagine situations in which it fails …

    I have clearly stated that I am not rejecting design. I am rejecting your argument for design based on pure chance calculations. But obviously, the point is not getting across.

  192. 192

    tribune7 at 174,

    Mustela — Design has unique characteristics. . .

    “That’s not a principle, it’s an assertion about an observation.”

    It’s an assertion of a principle. Do you accept or reject the claim?

    I reject the contention that it is a principle. You are claiming that designed objects have unique characteristics and that these characteristics are quantifiable.

    If you want to support your claim, identify at least one characteristic that is unique to designed objects and demonstrate how to measure that characteristic.

    Unless and until you can do that, your claim is baseless.

  193. Aleta– Your dismissal of ID is based on you being able to imagine situations in which it fails . . .I have clearly stated that I am not rejecting design.

    And I didn’t say you were. I said you were rejecting ID.

    And it’s been fun :-)

  194. Mustela — I reject the contention that it is a principle.

    OK, let’s take a step back. Do you believe that design exists?

  195. 195

    tribune7 at 196,

    Mustela — “I reject the contention that it is a principle.”

    OK, let’s take a step back. Do you believe that design exists?

    We have observed humans performing an activity we call design.

    I fail to see what you are trying to argue here. Either you have support for your claim that designed objects have unique, quantifiable characteristics or you do not. You can’t simply play word games and define objective observations into existence.

    Where is your evidence?

  196. Mustela — We have observed humans performing an activity we call design.

    I’ll take that as a yes.

    Is it possible to determine conclusively that there were things that came into existence due to this activity even though we did not witness the creation?

  197. 197
    material.infantacy

    h.pesoj: “Could I be sliently banned please?”

    If you want to be silently banned, there’s a procedure to follow:

    Step 1: Get in over your head while debating ID proponents.

    Step 2: Respond to questions with snarky jabs intended to score points with your peers on some other blog. These should be of the type which make it clear that you do not consider your opponents to be intellectual or cultural equals. If you are impressed with your own cleverness in these comments, chances are you’re hitting the mark.

    Step 3: Post inappropriate content to the moderation queue (yes you will need to be under moderation for this to work, so plan ahead). Do this until you are banned. This is really the crucial step, because it allows you to duck out of the conversation while saving face.

    Step 4: Claim the moral and intellectual high ground. This is really an extension of Step 3, and will require that at least some of your online peers are uncritical, servile groupies. Any discerning types will perceive the grift, although they will probably remain silent (you know, for the cause).

    Step 5: (Optional) Send a few lackeys over to make noise. These toadies should be the dull but loyal, expendable sort. The duller the better. You’ll probably have a few volunteers.

    Step 6: (Optional) Have your lackeys invent a moral indignity (this should be original!) such as “silent banning” and claim it as an offense.

    Good luck!

    ___________________________________

    Advertisement: To make a difference in the fight against silent banning, please make a donation to End Silent Banning Today. Make sure to include your mailing address in order to receive your chartreuse ribbon and permanent bumper sticker!

  198. As I said in another opening post, Ghost Hunters use the EF.

    backwards me:

    And what ghosts have they found then?

    Quite a few- just watch the show.

    However that is irrelevant. The point is the process works. It all depends on the people using it and the evidence they have.

  199. backwards me tghinking backwards:

    Not unless you’ve observed a designer creating life already.

    Science isn’t about absolute proof.

    The fact is life and the relationships beween the different branches of the tree of life look as we would expect them to if there was no designer other then evolution.

    Evolution isn’t being debated and it doesn’t predict any pattern.

    IOW your spewage is laid bare.

  200. designed objects have unique, quantifiable characteristic

    It’s called counterflow.

    And to refute the design inference just show that the observed counterflow is illusory.

  201. Aleta:

    And in No Free Lunch, despite what Dembski says about chance and necessity working together, the example he uses is just another calculation based on a pure chance arrangement of components.

    So what?

    Is he supposed to provide all examples?

    BTW coin flips take into account necessity- the coin has to fall.

    Dice- same thing.

    IOW Aleta your statement is meaningless.

  202. Jimmy Cagney

    We all know where this is going, see.

    Except it does not work, see.

    But I won’t be reading, see.

    Hiya, Jimmy.

  203. tribune7-

    (backwards me, Cala, Rob, Aleta are all knelling in front of Jimmy with their hands tied behind their back)

    We measure information with a dipstick, see.

    So now we’re going to measure the information between your ears, see.

    (blood-curdling screams in the background)

    This one is empty, see. Nothing on the ‘stick, see.

  204. Joseph,

    Oh be nice to Aleta. She wasn’t trolling. Neither was R0b, I think.

    Now the others . . . . .

  205. Thanks, Tribune. h.pesoj made it clear that he was trying to be provocative, but Mustala, Rob and me are, as far as I can tell, sincerely wanting to discuss the issues with people with whom we disagree in order to have the benefits, for ourselves and others, of a constructive dialog.

  206. 206

    tribune7 at 198,

    Mustela — “We have observed humans performing an activity we call design.”

    I’ll take that as a yes.

    Your question was “OK, let’s take a step back. Do you believe that design exists?”

    My response was intended to point out that your phrasing presumed the existence of some kind of platonic ideal of “design.” All we know for sure is that humans have been observed to design things. Design is a verb, an action, not a feature of an object.

    Is it possible to determine conclusively that there were things that came into existence due to this activity even though we did not witness the creation?

    You have claimed that it can be done, not just for some things but for any designed object. In fact, you have specifically claimed that design results in unique, quantifiable characteristics in the thing designed.

    What you have not done is to identify those characteristics or show how to measure them. I’ll repeat the part of my post 197 that you failed to address:

    Either you have support for your claim that designed objects have unique, quantifiable characteristics or you do not. You can’t simply play word games and define objective observations into existence.

    Where is your evidence?

  207. 207

    Aleta at 207,

    Thanks, Tribune. h.pesoj made it clear that he was trying to be provocative, but Mustala, Rob and me are, as far as I can tell, sincerely wanting to discuss the issues with people with whom we disagree in order to have the benefits, for ourselves and others, of a constructive dialog.

    That is certainly my intention. I don’t believe that any of my posts here could be objectively judged as trolling. I am genuinely interested in learning enough about CSI to be able to implement software to measure it.

    Frankly, I’m very surprised that this hasn’t been calculated and published by one of the ID luminaries. It would immediately refute a number of criticisms frequently leveled against ID.

  208. Mustela,

    My response was intended to point out that your phrasing presumed the existence of some kind of platonic ideal of “design.”

    But my phrasing does not presume that. I agree that design is an action — verb if you will. My point, however, is that it is a intrinsic part of reality and with which we interact.

    Design is . . . not a feature of an object.

    You seem to be saying designed objects don’t exist. Is that correct?

  209. 209

    tribune7 at 214,

    You seem to be saying designed objects don’t exist. Is that correct?

    You seem to be straining mightily to avoid supporting your claims. Allow me to repeat again:

    Either you have support for your claim that designed objects have unique, quantifiable characteristics or you do not. You can’t simply play word games and define objective observations into existence.

    Where is your evidence?

  210. Mustela

    You have claimed that it can be done, not just for some things but for any designed object.

    Actually, ID declares it won’t work with many if not most designed objects.

    But it is certainly something to ponder whether a methodology could be found that would ascertain any designed object.

  211. Mustela

    You seem to be straining mightily to avoid supporting your claims.

    You can’t even bring yourself to admit that designed objects exist. How can we have a discussion if you can’t agree to the obvious?

  212. 212

    tribune7 at 216,

    But it is certainly something to ponder whether a methodology could be found that would ascertain any designed object.

    Are you retracting your claims that designed objects have unique characteristics and that those are quantifiable?

  213. 213

    tribune7 at 217,

    You can’t even bring yourself to admit that designed objects exist.

    Your asking that question was just another evasion. They’re getting more and more transparent.

    Either you have support for your claim that designed objects have unique, quantifiable characteristics or you do not. You can’t simply play word games and define objective observations into existence.

    Where is your evidence?

  214. Mustela –

    Are you retracting your claims that designed objects have unique characteristics and that those are quantifiable?

    How do you get that from what I wrote in 216? The answer is no.

    You can’t even bring yourself to admit that designed objects exist. Your asking that question was just another evasion.

    If you can’t bring yourself to admit that designed objects exist, how can I expect you to see that they have quantifiable characteristics?

  215. 215

    tribune7 at 221,

    If you can’t bring yourself to admit that designed objects exist, how can I expect you to see that they have quantifiable characteristics?

    I have never claimed that designed objects do not exist. Your intimation that I have is disingenuous and another transparent attempt at distraction.

    I don’t mind beating my head against a wall if there’s a chance of breaking through, but I can tell brick when I feel it. You clearly have no support for your claims, nor do you intend to attempt to provide any. It also appears that you have no intention of retracting them.

    Given all that, my time is better spent looking for answers elsewhere. The floor is yours.

  216. Mustela, in 213 you said “Design is a verb, an action, not a feature of an object.”

    That can be taken as a claim that “design is . . not a feature of an object” since design is obviously a feature of a designed object this would appear to mean you don’t accept the existence of such things.

    I asked for clarification and you declined to give it — see post 216.

    So, you do accept the existence of designed objects? The discussion is pointless if you don’t.

  217. Mustela:

    I am genuinely interested in learning enough about CSI to be able to implement software to measure it.

    I told you how to measure it.

    IOW you are lying.

    In fact, you have specifically claimed that design results in unique, quantifiable characteristics in the thing designed.

    I answered that too.

    IOW it appears that you clowns are being overly selective.

    And that means you are lying when you say you come here to learn something about ID.

    All anyone really needs to do is go out and read the pro-ID literature.

  218. 218

    tribune7,

    h.pesoj is the same sock puppet as George L. Farquar. He’s no longer with us. I had previously banned him under George, and now he’s gone under his backwards “josep.h” name. Also, to whomever is interested, Voice Coil is no longer with us, because that was a sock puppet for Diffaxial, who I had previously banned. In short, they were both old sock puppets from the past, previously banned, and now banned again, nothing new to see here. :)

  219. Clive Hayden,
    You have, of course, every right to ban the likes of h.pesoj and Voice Coil, and it is helpful that you have given reasons for doing so. However I sense a certain irony when your explanation comes immediately after a comment by Joseph in which he calls his opponents clowns and liars. How long would an ID sceptic last here using that sort of approach?

  220. 220

    Joseph,

    IOW it appears that you clowns are being overly selective.

    Don’t be disrespectful or I will moderate you too. I am only concerned with the name calling, and I don’t care to hear any justification for it, just don’t do it.

  221. Ahhh Clive. I was starting to think of him as a pet. I’ll grant that he was starting to tinkle on the rug a bit much.

    material.infantacy sums it up well at 197 :-)

  222. 222

    tribune7,

    material.infantacy sums it up well at 197

    I think so too.

  223. Mustela @143:

    My comment #116 — especially the last para — was a response to our last conversation where I explained to you how to calculate CSI.

    You seem to not yet understand that there is no need, for the purpose of what is being calculated, for CSI to take into account the chemistry, physic, etc of our universe. CSI merely combines the number of specified patterns in a space of possibilities with the maximum number of bit operations that had passed until a specified pattern was discovered with the probability of finding that specified pattern given a uniform probability distribution. If a value > 1 results, we effectively have a “needle in a haystack” problem where, with the number of bit operations/flips available, we would not expect to find a specified event of that size. Add on to that the fact that we are indeed dealing with an event correlated to pattern, and we can see that chance (as explained in #127 above) — defined as lacking correlation — is not the best explanation. That is all that CSI is able to calculate. The calculation for CSI does not rule out law. That is why the Explanatory Filter is required. Refer to #127 above to see examples of chance, chance + law, and chance + law + intelligence.

    Then, refer to http://www.uncommondescent.com.....ent-337588 for a better explanation of the difference between law and organization such as CSI and how to objectively determine a specified pattern.

    I’ll end how I ended comment #116 above, since it appears to me that the last para in comment #116 should answer your question re: the relation between CSI and the laws of nature that exist within which we are measuring CSI …

    “CSI doesn’t “take into consideration” that our universe is fine tuned for life, since it is indeed the type of calculation that *shows us* that our universe is fine tuned for the evolution of life. CSI is the evidence of evolution (barring direct intervention) and evolution is the evidence of previous intelligence.”

    I’m looking forward to continuing this discussion with you, but I am “on and off” busy so I can’t guarantee time to set aside.

    To conclude for now, in the very least ID Theorists hypothesize that CSI will not be generated by law + chance absent intelligent fine tuning for future results. In order to falsify this, merely generate CSI or an evolutionary algorithm from a random set of laws without any intelligent input for future results. Random.org could come in very helpful for providing the random variables for the search space; and for the variables and formulas/algorithms for the laws.

  224. I guess that means once banned, forever banned. The door to heaven forever closed. No second chances here, nosiree! But was VC’s last post really that bad? One thing is not granting further access, but even disappearing what to me looked like a great post?

    Are we suffering from a culture collision?

  225. Cabal — I guess that means once banned, forever banned.

    Apparently not, as Clive pointed out in Post 218.

    Also, check out post 197. There were apparently things going on behind the scene in the mod queue.

  226. 226

    CJYman at 223,

    My comment #116 — especially the last para — was a response to our last conversation where I explained to you how to calculate CSI.

    You seem to not yet understand that there is no need, for the purpose of what is being calculated, for CSI to take into account the chemistry, physic, etc of our universe.

    Actually, I would argue that it is you who does not understand that it is essential for CSI to take known physics, chemistry, and evolutionary mechanisms into account if it is to be a useful measure in the real world. The reason for this, as I explained in our previous discussion, is where ignoring these factors leads:

    “CSI merely combines the number of specified patterns in a space of possibilities with the maximum number of bit operations that had passed until a specified pattern was discovered with the probability of finding that specified pattern given a uniform probability distribution.

    Your assumption of a uniform probability distribution is invalid. The only way to make such an assumption is to ignore known physics, chemistry, and evolutionary mechanisms, which makes the result of any calculation inapplicable to the real world we live in.

    Dembski recognizes this in No Free Lunch where he mentions the need to take all known natural causes into account.

    Just to give an example of why it is essential to take known science into account, consider the issue of identifying the change in CSI due to a mutation. Using a naive, two to the power of the length of the genome calculation, point mutations result in no additional CSI, even though they may change the result of transcribing the genome, while frame shifts, insertions, and deletions change the length, and therefore the CSI, without necessarily changing the function of the genome.

    So, I’m afraid you still haven’t provided an example of how to calculate CSI for a real biological system. I do hope you’ll continue the discussion as time permits. It might be most productive to start with the specification and then work on the actual calculation.

  227. So, I’m afraid you still haven’t provided an example of how to calculate CSI for a real biological system.

    Other people, including myself, have done just that.

    That you choose to ignore what has already been said just proves that you are not worth the effort.

    When people talk of “evolutionary mechanisms” it is a sure sign that they don’t know what they are talking about.

    Ya see evolutionary mechanisms did not exist until living organisms appeared.

    Also, as far as anyone knows, the bulk of evolutionary mechanisms are in fact design mechanisms.

    Dr Spetner went over that 13 years ago.

    Also CSI does take into account physics, chemistry and evolutionary mechansims.

    To say otherwise is to prove your ignorance of the topic.

    But anyway the laws of physics and chemistrt are part of what needs explaining.

    IOW by weasel man trying to use them to weasel through an argument just further exposes the ignorance.

  228. 228

    Cabal,

    “But was VC’s last post really that bad?”

    He shouldn’t have been posting here at all, I had previously banned him under Diffaxial. I don’t care for sock puppets, and I don’t care for the martyrdom of sock puppets who continually merit banning. I’ve noticed a tendency to this behavior, mostly by folks from that absurd “after the bar closes” site, to push the envelope, sometimes subtly, all the while expecting great accolades from their cleverness with their dull cohorts at that other site, and then cry “unfairness” when they are no longer allowed to be mocking here. I have no respect for this very strange, and quite honestly cowardly, behavior. They’re like bad seed children, who intentionally cause mischief and then cry when they’re punished, as if to say “Why did you punish me, you know I’m only a child” and then play the victim role. I’ve seen it over and over.

  229. (long time lurker here). Joseph, I’ve read Dembski’s work backwards and forwards, but I’ve never seen him offer a workable criteria for CSI. Notably, in his equation for CSI,

    ? = – log2[10^120 ·?S(T)·P(T|H)]

    he has the term ?S(T), where

    ?S(T) is a multiplier based on the number of similarly simply and independently specifiable targets

    So, say we were trying to look at the probability of a simple amoeba occurring “by chance” (this is a bit of a strawman for evolution’s position, but just for the sake of discussion). We’d need to know not only the length of the chromosome, but the number of different ways the genes on the chromosome could be arranged, as well as the number of variants each gene could have. For any gene, there are many alternate base code sequences that would produce the same protein, and many proteins are also somewhat robust to having their amino acids switched. So this term, ?S(T), makes the equation impractical, as there is no practical way to know just how many possible variants there are.

    This is why Dembski’s definition of CSI is useless – if I were to give you a 500 bit sequence of DNA, would you be able to tell me whether it was functional and useful? Could anyone do this? Because without this, there’s no way of telling just how “specified” a DNA sequence needs to be useful, and so you can’t know if it violates the UPB.

  230. Tribune, I accept the existence of designed objects, but I don’t see that there’s any sure way to tell what parts of DNA are designed or not. All of the experience of archaeologists and SETI-astronomers are useless here; they’re dealing with quite different situations. SETI experts are looking for the signs of alien life with the assumption that they *want* to be found and are broadcasting radio waves in regions of the spectrum where there would be no natural noise. Archaeologists look for well-established antecedents to today’s technology. This is trivial, since we *know* what designed pottery looks like and have never seen any natural processes that could produce painted and fired ceramics. Biology’s a different story, though, since we don’t know what designed DNA would look like. Of course, a designer could have made it obvious, by putting in a nice sequence of prime numbers written in our DNA, or something similar to say “this was designed”. But there’s nothing like that that we’ve found.

  231. Ben W-

    We observe the specification/ functionality.

  232. Mustela @226,

    It appears that we are speaking past each other, since I’ve adequately answered the questions that you continue to post. It seems that you have some idea of what CSI is “supposed” to tell which is not in fact what CSI *does actually* tell us.

    CJYman:
    “You seem to not yet understand that there is no need, for the purpose of what is being calculated, for CSI to take into account the chemistry, physic, etc of our universe.”

    Mustela:
    “Actually, I would argue that it is you who does not understand that it is essential for CSI to take known physics, chemistry, and evolutionary mechanisms into account if it is to be a useful measure in the real world. The reason for this, as I explained in our previous discussion, is where ignoring these factors leads:”

    Well then go ahead and edumacate me. Argue for your understanding of CSI and explain to me each variable in the equation for CSI and tell me what combining the variables tells us. This will probably be a more profitable way to continue our discussion.

    CJYman:
    “CSI merely combines the number of specified patterns in a space of possibilities with the maximum number of bit operations that had passed until a specified pattern was discovered with the probability of finding that specified pattern given a uniform probability distribution.”

    Mustela:
    “Your assumption of a uniform probability distribution is invalid.”

    There is no such assumption. The uniform probability distribution is included so that if we arrive at a > 1 value, we have strong evidence that we are indeed *not* dealing with a uniform probability distribution. Then, the NFL Theorems take over to continue the argument.

    Mustela:
    “The only way to make such an assumption is to ignore known physics, chemistry, and evolutionary mechanisms, which makes the result of any calculation inapplicable to the real world we live in.”

    What assumption??? It appears that you indeed do not understand CSI.

    Mustela:
    “Dembski recognizes this in No Free Lunch where he mentions the need to take all known natural causes into account.”

    You’re correct in a sense. Natural causes are reducible to law and chance and, I would add, intelligence. But, I differ with what appears to be Dembski’s position at the time he wrote NFL. I don’t see law as a category within chance because of how the patterns I showed in #127 can be categorized.

    CSI only take the natural cause “chance” into consideration. Since statistical randomness is equated with chance, the measure against a uniform probability distribution is included in the formula. Again, as I’ve stated a few time already, a > 1 value provides strong evidence that a uniform probability distribution, and thus chance, can be effectively eliminated.

    As I wrote above, and you either ignored, didn’t read, or didn’t understand, CSI does not rule out law without the application of the Explanatory Filter. CSI only rules out chance, thus providing evidence against those who think that life started out as some sort of chance arrangement of molecules.

    Mustela:
    “Just to give an example of why it is essential to take known science into account, consider the issue of identifying the change in CSI due to a mutation. Using a naive, two to the power of the length of the genome calculation, point mutations result in no additional CSI, even though they may change the result of transcribing the genome, while frame shifts, insertions, and deletions change the length, and therefore the CSI, without necessarily changing the function of the genome.”

    Tell me, Mustela, can you provide any evidence that the system required to utilize all those processes can be generated absent intelligence? Of course, CSI can be measured at any point, so give me an example of what you are talking about, including all the “givens.” Ie: given a living system, x amount of time, and gene x, what transformations can be reasonably arrived at by chance. BTW, there seems to be evidence that evolution can be guided by laws that emerge from the organization of living systems. Organized (as opposed to “ordered” — as explained in the link I’ve already included for you above) CSI can not reasonably be arrived at by chance + law absent intelligence, but that by no means indicates that chance + law are not utilized in the process of arrive at CSI. Is this making sense? Remember that evolutionary algorithm are the best example of law + chance + intelligence working together. Intelligence provides the foresight by utilizing knowledge of the future target to fine tune parameters in the present, and law and chance do the dirty work by directing the search through the possibilities toward targets as the program unfolds.

    Mustela:
    “So, I’m afraid you still haven’t provided an example of how to calculate CSI for a real biological system. ”

    I’m not sure what type of “CSI” you are talking about, but I most definitely have provided an estimated value for the lowest amount of CSI possible for the protein Titin. The probabilistic resources are actually horribly inflated in favor of the ID critic, however that is for another discussion. So, back to what we are talking about, it seems that your qualm is not in merely applying the formula for CSI but in the implications of CSI. Furthermore, you seem to think it implies much more than it really does, which I have attempted to clear up earlier in this comment.

    Mustela:
    “I do hope you’ll continue the discussion as time permits. It might be most productive to start with the specification and then work on the actual calculation.”

    I’m enjoying this discussion as you seem to be one of the rare ID critics, along with ROb and Nakashima (off the top of my head), who is actually interested in discussing ID rather than muddying the conversation with obfuscation.

    Give me an event, and we can start by discussing the specification if it does indeed exist.

  233. CJYman, thank you. In fairness, I think that many ID opponents are interested in clarifying rather than obfuscating the issues. In my opinion, critics such as Wein, Elsberry & Shallit, Tellgren, and Haggstrom epitomize lucidity.

    WRT CSI, Dembski’s current definition is:

    –log2[10^120 * ΦS(T) * P(T|H)]

    When he applies this to bacterial flagella, he said that H is “the relevant chance hypothesis that takes into account Darwinian and other material mechanisms.”

    Dembski also says:

    Suppose the relevant collection of chance hypotheses that we have good reason to think were operating if the event E happened by chance is some collection of chance hypotheses {Hi}i ∈ I indexed by the index set I. Then, to eliminate all these chance hypotheses, Χi = –log2[10^120 * ΦS(T)*P(T|Hi)] must be greater than 1 for each Hi.

    I don’t know how it could be any clearer that we need to look at all relevant chance hypotheses, not just uniform randomness.

  234. Joseph, at the very most we observe the functionality of a few of the 2^500 possibilities inherent in a 500-bit piece of DNA. But we can’t know the ?S(T) if we can’t determine how useful the other combinations are.

    I’ll use an analogy to Battleship. We’re trying to find out how good our odds are for hitting a battleship. We’ve got a space to guess that’s 2^500 big (about 10^150 possible guesses). We know a few of the spaces where we’ve “hit”, but we don’t know anything about the rest of the map. It’s a pretty big search space.

    Now, Dembski says that because it’s such a big search space, the first few “hits” we got were placed by someone with knowledge of our opponent’s board, that you could never get these by random chance, not even over the history of the universe. But Dembski also includes that term phi*S(T), which is the number of spaces on the opponent’s board that is filled with battleships. For obvious reasons, this number affects the probability calculation. It’ll be much easier to hit a battleship by random chance if the opponent’s board is 99% full vs. 1% full. Heck, if even 1 spot in 10^8 had a battleship, it’d still be both rare and well within the range of evolution – since evolution also has time on its side. But nobody really knows how big Phi*S(T) is, including Dembski.

    Savvy?

  235. 236

    CJYman at 233,

    It appears that we are speaking past each other, since I’ve adequately answered the questions that you continue to post. It seems that you have some idea of what CSI is “supposed” to tell which is not in fact what CSI *does actually* tell us.

    My understanding from No Free Lunch and other reading is that CSI is supposed to be a unique characteristic that identifies designed objects. Is that your understanding as well?

    CJYman:
    “CSI merely combines the number of specified patterns in a space of possibilities with the maximum number of bit operations that had passed until a specified pattern was discovered with the probability of finding that specified pattern given a uniform probability distribution.”

    Mustela:
    “Your assumption of a uniform probability distribution is invalid.”

    There is no such assumption.

    I’m confused, you state that assumption explicitly in your definition.

    The uniform probability distribution is included so that if we arrive at a > 1 value, we have strong evidence that we are indeed *not* dealing with a uniform probability distribution. Then, the NFL Theorems take over to continue the argument.

    That’s exactly why the assumption of a uniform probability distribution is invalid. The NFL theorems say that any particular search algorithm is no better than random search when averaged over all possible domains. It says nothing about the efficacy of a particular search algorithm in a particular domain. The real world is a particular domain, and the only one of interest. Known evolutionary mechanisms are observed to be an effective search algorithm (leaving aside the discussion of whether or not this is a good model for what we’re discussing) in the real world.

    Therefore, assuming a uniform probability distribution ignores what we know about both the algorithm and the domain and is hence inapplicable to observed phenomena. That inapplicability eliminates the ability of CSI, formulated as above, to uniquely characterize a designed object.

    Mustela:
    “Dembski recognizes this in No Free Lunch where he mentions the need to take all known natural causes into account.”

    You’re correct in a sense. Natural causes are reducible to law and chance and, I would add, intelligence. But, I differ with what appears to be Dembski’s position at the time he wrote NFL. I don’t see law as a category within chance because of how the patterns I showed in #127 can be categorized.

    Is your definition of CSI different from Dembski’s, then? ROb quotes Dembski in 234 as requiring that “Darwinian and other material mechanisms” be taken into account. The assumption of a uniform probability distribution fails to do that.

    Mustela:
    “I do hope you’ll continue the discussion as time permits. It might be most productive to start with the specification and then work on the actual calculation.”

    I’m enjoying this discussion as you seem to be one of the rare ID critics, along with ROb and Nakashima (off the top of my head), who is actually interested in discussing ID rather than muddying the conversation with obfuscation.

    Thanks for the kind words. Given both of our schedules, I suspect we’ll be chasing this issue around multiple threads before we’re done. You’re my best hope for implementing a CSI calculator in software!

    Give me an event, and we can start by discussing the specification if it does indeed exist.

    From another thread, I’d suggest the specification of citrate digestion in Lenski’s e. coli, if that makes sense. Determining the CSI before and after that functionality manifested would be very interesting.

  236. Mustela:
    “My understanding from No Free Lunch and other reading is that CSI is supposed to be a unique characteristic that identifies designed objects. Is that your understanding as well?”

    Technically, and this is what needs to be understood in order to develop an ID argument, CSI only effectively rules out the chance hypothesis which is what I’ve been trying to explain to you above. Then, upon applying the EF in the mode that I’ve also explained above via the given link, one can identify a designed object.

    Mustela:
    “I’m confused, you state that assumption explicitly in your definition.”

    There is no assumption of a uniform probability distribution — there is a measurement against a uniform probability distribution. Did I not explain this adequately? The only “assumption,” or rather valid representation, is that chance is modeled by statistical randomness and that a uniform probability distribution = a random/chance distribution. Are you seeing yet how a value > 1 shows us that the search space is not uniform?

    Mustela:
    “That’s exactly why the assumption of a uniform probability distribution is invalid.”

    The only assumption is that chance hypothesis = uniform probability distribution. But, as I’ve stated above, that’s not really “just an assumption,” since a uniform probability distribution is the concept of statistical randomness, and thus chance, applied to a search space.

    Mustela:
    “The NFL theorems say that any particular search algorithm is no better than random search when averaged over all possible domains.”

    Yes …

    Mustela:
    “It says nothing about the efficacy of a particular search algorithm in a particular domain.”

    Incorrect. An efficient search requires a fortuitous matching between search space and search algorithm. That’s pretty much the whole point of the NFL Theorems when I last read through them. But this is going beyond CSI. Let’s clear up our understanding of CSI first before we head out into deeper waters.

    Mustela:
    “The real world is a particular domain, and the only one of interest.”

    That depends on what you mean by “only one of interest.” Physicists have been and are interested in discovering how fine tuned our laws are to support any type of living and furthermore intelligent organism, in relation to all possible mathematical values for the equations which describe our laws. Remember, there is as of yet no reason why our laws have to, as a matter of necessity, have the values which they do have. You may not find this, and the resulting calculations which only match intelligently produced events, interesting but myself and others sure do find this extremely interesting and amenable to research utilizing computers and math. In fact, Seth Lloyd has hypothesized that our universe is literally a quantum computer (“Programming the Universe”).

    But, yes, we only have a sample size of 1 for universes. That is the size which is used for the probabilistic resources in the calculation for CSI, since anything further out from our light cone could not effect events here if state changes (information) can indeed not travel faster than light.

    Mustela:
    “Known evolutionary mechanisms are observed to be an effective search algorithm (leaving aside the discussion of whether or not this is a good model for what we’re discussing) in the real world.”

    No, we must not “leave that aside.” It is integral to our discussion. But, as I said, let’s pin down our understanding of CSI first before delving deeper.

    Mustela:
    “Therefore, assuming a uniform probability distribution ignores what we know about both the algorithm and the domain and is hence inapplicable to observed phenomena.”

    Incorrect, as it is the measurement of CSI which provides evidence that (barring direct intervention) we require an evolutionary algorithm to produce the given event. Did I not explain this earlier? You seem to be operating under some sort of assumption that CSI = no evolution is possible. Is this true?

    Mustela:
    “That inapplicability eliminates the ability of CSI, formulated as above, to uniquely characterize a designed object.”

    What inapplicability? CSI is merely a measurement of probabilistic resources, and specificity against a uniform probability distribution. The uniform probability distribution merely acts as a sort of “zeroing;” a calibration. Thus, if we can measure for probabilistic resources and specificity, we can measure the event against a uniform probability distribution. Is it getting clear now how a value > 1 only tells us that the event is generated from a non-uniform probability distribution? Thus, there is some type of stepping/ratcheting/evolutionary process which can be utilized if the proper search procedure can be matched to the underlying ordered/organized/non-uniform search space.

    Are you saying that you can provide evidence that chance + law absent intelligent foresight, fine tuning for future results, will produce CSI? On the other hand, I can and have provided evidence in the above links that chance + law, absent intelligence, will not produce organized CSI. Furthermore, I can also show that events known to have required foresight in their construction are definable in terms of organized CSI.

    Science works by putting 2 and 2 together. After all, it is through that type of observation, inference, and extrapolation into the past that also provides evidence for the evolution of life.

  237. Mustela:
    “Is your definition of CSI different from Dembski’s, then? ROb quotes Dembski in 234 as requiring that “Darwinian and other material mechanisms” be taken into account. The assumption of a uniform probability distribution fails to do that.”

    There do seem to be a few areas where I disagree with Dembski … or at least some of his viewpoints in the past. I think that quote above is from before Dembski realized that evolution itself — even of the technically Darwinian type — is evidence of previous intelligence, which is something he definitely believes now as shown in his recent works.

    I have a question for you. Are all those “material mechanisms” you cite above, chance based? IE: are HGT, point mutations, duplicate genes, etc. random occurences? Or are they sometimes guided by the structure of life — from the laws that emerge from life’s organization?

    Looking forward to hearing from you again. Creating a CSI calculator would actually be quite simple. Collecting the data for the variables is the hard, yet very interesting, part.

  238. “Creating a CSI calculator would actually be quite simple”

    Cool! Maybe someone can set it up as a server on this site. It would be a great resource for those of us less code-minded…..

  239. CJYman:

    Technically, and this is what needs to be understood in order to develop an ID argument, CSI only effectively rules out the chance hypothesis which is what I’ve been trying to explain to you above.

    To say “the chance hypothesis,” as if there is only one, makes no sense in Dembski’s framework. As I quoted in 179, Dembski explains, “Chance as I characterize it thus includes necessity, chance (as it is ordinarily used), and their combination.” And as I showed in 234, Dembski says that all relevant chance hypotheses need to be eliminated.

    Then, upon applying the EF in the mode that I’ve also explained above via the given link, one can identify a designed object.

    According to Dembski, traversing the EF is the same as ascertaining specified complexity. (Quote available on request.) They are not two different steps in detecting design.

    I think that quote above is from before Dembski realized that evolution itself — even of the technically Darwinian type — is evidence of previous intelligence, which is something he definitely believes now as shown in his recent works.

    Actually, the quote is from his 2005 paper, which he called his “most up-to-date treatment of CSI” in December 2008. His belief that Darwinian evolution is evidence of design goes back to at least 2002. I don’t have NFL on hand, but speaking of that book, Dembski said, “Why is ours a world where the Darwinian mechanism works (if indeed it works)? In NFL I contend that design looms here as well.”

    When we get into the logic of using the NFL principle for inferring design, I’ll have more to say about it. For now, I’ll just point out that Dembski and Marks’ reasoning hinges on the assumption that all causal chains are ultimately rooted in uniform distributions over certain spaces, and that the only support they offer for this assumption is Bernoulli’s PrOIR.

  240. 241

    CJYman at 237,

    “My understanding from No Free Lunch and other reading is that CSI is supposed to be a unique characteristic that identifies designed objects. Is that your understanding as well?”

    Technically, and this is what needs to be understood in order to develop an ID argument, CSI only effectively rules out the chance hypothesis

    This isn’t my understanding from No Free Lunch, other papers, and other ID proponents on this site. When you say “chance hypothesis” do you mean “de novo creation”? If so, that’s not particularly interesting because no biologist claims that real biological artifacts arise de novo. If by “chance hypothesis” you mean “non-intelligent causes” then your assumption of a uniform probability distribution ignores known physics, chemistry, and evolutionary mechanisms and so is also not applicable to the real world.

    Then, upon applying the EF in the mode that I’ve also explained above via the given link, one can identify a designed object.

    If the Explanatory Filter is where known physics, chemistry, and evolutionary mechanisms are taken into consideration, it cannot use a uniform probability distribution either. I didn’t see anything in your calculations that make them applicable in the real world.

    “I’m confused, you state that assumption explicitly in your definition.”

    There is no assumption of a uniform probability distribution — there is a measurement against a uniform probability distribution. Did I not explain this adequately?

    Are we using the word differently? I am using “assumption” in the mathematical sense. When you choose to measure against it, you are most definitely assuming a uniform probability distribution.

    The only “assumption,” or rather valid representation, is that chance is modeled by statistical randomness and that a uniform probability distribution = a random/chance distribution.

    It’s deeper than that, though. By measuring against a uniform probability distribution, you are implicitly assuming that such a distribution reflects some aspect of the real world. As I’ve repeatedly pointed out, it does not because it fails to take into account known physics, chemistry, and evolutionary mechanisms. Those factors make the actual probability distribution of particular biological artifacts far from uniform.

    Are you seeing yet how a value > 1 shows us that the search space is not uniform?

    We already know the search space isn’t a uniform probability distribution because we know about physics, chemistry, and a number of evolutionary mechanisms.

    “The NFL theorems say that any particular search algorithm is no better than random search when averaged over all possible domains.”

    Yes …

    “It says nothing about the efficacy of a particular search algorithm in a particular domain.”

    Incorrect.

    I’m afraid I must disagree. What I wrote is exactly correct. You can read the papers (sorry, link didn’t work) to confirm that.

    An efficient search requires a fortuitous matching between search space and search algorithm.

    Our search space is a given: the real world. Observation shows that evolutionary mechanisms work well in that environment.

    “The real world is a particular domain, and the only one of interest.”

    That depends on what you mean by “only one of interest.” Physicists have been and are interested in discovering how fine tuned our laws are to support any type of living and furthermore intelligent organism, in relation to all possible mathematical values for the equations which describe our laws.

    We’re talking about evolution, not physics. I think I mentioned during one of our last discussions that you might be able to make a case for cosmological ID using the NFL theorems, but they are completely inapplicable when discussing the evolution that is observed in the one biosphere we know about.

    “Therefore, assuming a uniform probability distribution ignores what we know about both the algorithm and the domain and is hence inapplicable to observed phenomena.”

    Incorrect, as it is the measurement of CSI which provides evidence that (barring direct intervention) we require an evolutionary algorithm to produce the given event.

    CSI is supposed to show that intelligent intervention is required for a particular biological artifact to exist. In order to do that, it must rule out known natural causes such as known evolutionary mechanisms. When a uniform probability distribution is assumed, those known natural causes are ignored, making any calculation inapplicable to the real world.

    Did I not explain this earlier? You seem to be operating under some sort of assumption that CSI = no evolution is possible. Is this true?

    My understanding is that the presence of CSI is supposed to be a clear and unambiguous indication that non-intelligent mechanisms are insufficient to explain the artifact under consideration. While some non-intelligent mechanisms may be involved, CSI is supposed to show that something else is also required.

    I can and have provided evidence in the above links that chance + law, absent intelligence, will not produce organized CSI.

    With all due respect, I don’t think you have. Your calculations don’t correspond to CSI as described in No Free Lunch and changes in the length of a genome, for example, can be explained by known types of mutations.

    Furthermore, I can also show that events known to have required foresight in their construction are definable in terms of organized CSI.

    I would like to see that calculation.

  241. 242

    CJYman at 238,

    “Is your definition of CSI different from Dembski’s, then? ROb quotes Dembski in 234 as requiring that “Darwinian and other material mechanisms” be taken into account. The assumption of a uniform probability distribution fails to do that.”

    There do seem to be a few areas where I disagree with Dembski … or at least some of his viewpoints in the past. I think that quote above is from before Dembski realized that evolution itself — even of the technically Darwinian type — is evidence of previous intelligence, which is something he definitely believes now as shown in his recent works.

    Could you point me to a cite?

    This sounds more like a cosmological ID argument than an evolutionary ID argument. Showing that intelligence is required for evolution to result in the diversity of life we see is different from showing that evolutionary mechanisms (and presumably the underly physics and chemistry) require intelligent intervention.

    I have a question for you. Are all those “material mechanisms” you cite above, chance based? IE: are HGT, point mutations, duplicate genes, etc. random occurences? Or are they sometimes guided by the structure of life — from the laws that emerge from life’s organization?

    Mutations are generally assumed to be random with respect to fitness, and bad mutations are culled by natural selection, which is not a random process. There is some interesting work being done on the evolution of evolvability and variable evolvability, which is quite interesting but doesn’t negate the basic concepts.

    Looking forward to hearing from you again. Creating a CSI calculator would actually be quite simple. Collecting the data for the variables is the hard, yet very interesting, part.

    I hope you’re right, but I think we still a ways off from a mathematically rigorous algorithm.

  242. ROb @ 240,

    I’ve already addressed where I disagree with Dembski on law being a subset of chance. Law can’t be a subset of chance if Dembski is correct that CSI adequately refutes the chance hypothesis. That is because law is defined by compressibility and a long enough compressible pattern will produce CSI. Thus, the EF is required to arrive at what I have dubbed organized CSI — designed objects (melding Dembski’s CSI with Treveor and Abel’s “organization.”)

    The main point is extremely simple to follow and understand…

    ahh0duhdu’;g nznb — defined and thus best explained by chance. Algorithmically complex and statistically random.

    aaaaaaaaaaaa or afdsafdsafdsafds — defined and thus best explained by chance + law. Algorithmically compressible with an element of chance for the set of laws utilized and which letter(s) is/are utilized.

    “DO you understand me?” — defined and thus best explained by chance + law + intelligence. Algorithmically complex, specified, sufficiently complex (improbable) in the context of this comment; foresight for communication required; historical contingency of the English language and our conversation shows how chance is included in the explanation; able to have arrived via evolutionary algorithm, thus the potential for law as an included explanation.

  243. Mustela:
    “This isn’t my understanding from No Free Lunch, other papers, and other ID proponents on this site.”

    You expect everyone to have the exact same understanding? You do realize not everyone understands or has the same hypothesis for evolution, right? So, why demand anything different as it pertains to ID Theory? At the end of the day, whichever hypothesis works the best will be used.

    Mustela:
    “When you say “chance hypothesis” do you mean “de novo creation”?”

    What else can you offer that utilizes only chance? Evolutionary algorithms sure don’t work only by chance.

    Mustela:
    “If so, that’s not particularly interesting because no biologist claims that real biological artifacts arise de novo.”

    Now, it looks like we are on the same page. The really interesting thing is not that biologists already intuitively know what the measurement for CSI tells us — although the fact that the specificity and complexity can be quantified is indeed interesting — but that no one to date has falsified or provided any theoretical underpinning to show that organized CSI can be generated absent previous intelligence through computational simulations.

    Mustela:
    “If by “chance hypothesis” you mean “non-intelligent causes” then your assumption of a uniform probability distribution ignores known physics, chemistry, and evolutionary mechanisms and so is also not applicable to the real world.”

    First, it should be obvious by now that I don’t see law as a subset of chance, yet law is a non-intelligent cause.

    I thought I already defined chance earlier a few times … you know … uniform probability distribution, statistical randomness, lacking correlation, and unguided by rules or lawful constraints.

    Mustela:
    “If the Explanatory Filter is where known physics, chemistry, and evolutionary mechanisms are taken into consideration, it cannot use a uniform probability distribution either.”

    I’m sorry, but now this is turning into ID 101 and you should really do some research on the basic concepts of ID Theory. I’d love to explain ID Theory and my own hypothesis, but I just don’t have the time.

    Very briefly, the EF doesn’t “use a uniform probability distribution.” The EF merely states that one must effectively rule out chance and then law in order to label a given event as intelligently designed. CSI rules out chance very effectively, and my previous explanation of organization rules out law — same type of idea as “the physics and chemistry (laws) of the ink and paper do not define the pattern and meaning within an essay.”

    Mustela:
    “I didn’t see anything in your calculations that make them applicable in the real world.”

    You didn’t notice how the calculation rules out a uniform probability distribution if a value > 1 results?

    Mustela:
    “Are we using the word differently? I am using “assumption” in the mathematical sense. When you choose to measure against it, you are most definitely assuming a uniform probability distribution.”

    Ah, yes, I see now. In a mathematical sense, we are “assuming” a uniform probability distribution in order to see if our assumption is correct. Given a uniform probability distribution, we will not get a value > 1, so if that > 1 value results, we know that we are not dealing with a uniform probability distribution. Simple as that.

    Mustela:
    “It’s deeper than that, though. By measuring against a uniform probability distribution, you are implicitly assuming that such a distribution reflects some aspect of the real world.”

    Yes, there are such thing as uniform probability distributions.

    Mustela:
    “As I’ve repeatedly pointed out, it does not because it fails to take into account known physics, chemistry, and evolutionary mechanisms. Those factors make the actual probability distribution of particular biological artifacts far from uniform.”

    I’ve already dealt with this repeated “fact” of yours and you seem to be ignoring my response, or at least not understanding it. If I am being unclear, please ask for clarification on the issue.

    Your understanding of the problem is lacking. Physics and chemistry on their own do no such thing, since the patterns we are discussing are not defined by the laws of physics and chemistry. If law did effect the sequencing of nucleotides, then they would not be able to carry information. We would merely be stuck with a repeating structure such as ACTGACTGACTG, which would then be defined and explained by chance + law, much like a crystal or a snowflake.

    And yes, CSI does not take evolutionary mechanisms into account. As I already stated before, CSI itself is evidence of evolution for the main fact that CSI tells us that (barring direct intervention) we are dealing with a non-uniform probability distribution being matched with a correct search algorithm for efficient search.

    Mustela:
    “We already know the search space isn’t a uniform probability distribution because we know about physics, chemistry, and a number of evolutionary mechanisms.”

    So, your main point is that CSI is redundant? I can see why you might say that, however, CSI actually gives us the quantification of an event that requires either direct intervention or an evolutionary algorithm. So, as far as providing a measurement, and providing evidence for evolution, CSI is not redundant.

    Mustela:
    “I’m afraid I must disagree. What I wrote is exactly correct. You can read the papers (sorry, link didn’t work) to confirm that.”

    I’ve already read through the paper a few times and the authors explicitly state what I said. I can provide a few quotes upon request.

    Mustela:
    “Our search space is a given: the real world. Observation shows that evolutionary mechanisms work well in that environment.”

    Yes, because, according to the NFL Theorems, there has been a “fortuitous” matching between a non-uniform probability distribution and search algorithm (relying upon the structure and information processing ability of life itself). If you want to provide evidence against the ID position, merely show that the above can be accomplished through only law + chance, absent intelligence. IOW, merely show me that CSI can be generated absent previous intelligent (foresighted for a future target) input.

    Mustela:
    “We’re talking about evolution, not physics. I think I mentioned during one of our last discussions that you might be able to make a case for cosmological ID using the NFL theorems, but they are completely inapplicable when discussing the evolution that is observed in the one biosphere we know about.”

    I have been making a case for cosmological ID this whole time, and it is wholly dependent on the CSI calculated of systems within our universe — ie: the biosphere that we know about. If CSI was not calculated in living systems, then an evolutionary algorithm wouldn’t be necessary and there would be no argument for ID Theory in life based on specificity and complexity (improbability) at the biosphere level or the cosmological level. NFL Theorems are absolutely applicable to life, and evolution on our planet, since they imply accounting principles when it comes to the generation of efficiently produced [and specified or pre-specified] events — CSI.
    IMO, there is no good case for direct intervention in abiogenesis, life, or evolution.

    Mustela:
    “CSI is supposed to show that intelligent intervention is required for a particular biological artifact to exist.”

    I emphatically disagree!!!!!!! CSI requires no intervention as long as an evolutionary algorithm of any type can account for said pattern. Although, I am beginning to realize that a CSI calculation > 1 between two functional patterns, with a sea of “nonfunction” in between them, would definitely provide evidence against a purely darwinian account of evolution. But, this is really old hat, now that modern evolutionary research seems to be providing evidence that self-guided genetic engineering within life is most likely also responsible, along with darwinian random mutations, for evolution. Furthermore, there seem to be a fair amount of scientists who argue that natural selection hinders rather than helps evolution in certain contexts. But that is definitely for another discussion. Back to CSI …

    Mustela:
    “In order to do that, it must rule out known natural causes such as known evolutionary mechanisms. When a uniform probability distribution is assumed, those known natural causes are ignored, making any calculation inapplicable to the real world.”

    I’ve adequately responded to that line of incorrect understanding above in previous comments (I’m quite sure) and definitely above within this comment.

    We seem to be going around in a circle now, and I’m beginning to notice that I’m repeating myself and you seem to be ignoring some of my explanations and clarifications. For the record, I hate having to repeat myself if my responses are being ignored. It wastes too much of my time and tells me that we aren’t going to get any further in our discussion.

    Simply, CSI provides evidence for evolution; it does not “rule out” evolution.

    Mustela:
    “My understanding is that the presence of CSI is supposed to be a clear and unambiguous indication that non-intelligent mechanisms are insufficient to explain the artifact under consideration.”

    Almost bang on, except that could be misinterpreted. A robot in a car factory could be seen as non-intelligent. That robot is sufficient to a certain extent in explaining the existence of cars.
    However, cars would not exist without intelligence, since that robot would also not exist without intelligence. IOW, that robot is neither defined by nor best explained by chance + law, absent intelligence. An evolutionary algorithm is really just an efficient search robot.

    A simple way to understand the implication of CSI is that it provides a clear and unambiguous indication that the artifact under consideration can not be generated by chance + law, absent previous intelligence in that artifact’s causal chain.

    Mustela:
    “While some non-intelligent mechanisms may be involved, CSI is supposed to show that something else is also required.”

    Correct … Intelligence is required somewhere down the causal chain.

    Mustela:
    “With all due respect, I don’t think you have. Your calculations don’t correspond to CSI as described in No Free Lunch…”

    My calculations are based on Demsbki’s definition of a specified event being an event which can be formulated as an independent pattern, and all calculations coincide with his most up to date explanation of CSI as posted on his website under the paper “Specifications: the Patterns which Signify Intelligence.”

    A more in depth look at why CSI effectively eliminates chance can be found at http://www.angelfire.com/pro/k.....htm#fsciis, especially in table of contents points A] and B].

    Mustela:
    “…and changes in the length of a genome, for example, can be explained by known types of mutations.”

    And because they are “known types of mutations” means what exactly in light of calculating for CSI?

    Again, if you don’t think that CSI points to intelligence, I suggest you use less words and merely provide evidence that chance + law absent previous intelligence will generate CSI. Until then, that ID hypothesis is standing strong.

  244. This is way off topic but since the phrase No Free Lunch was just mentioned, here are a couple things someone just sent me.

    —————–
    Who said there was no such thing as a Free Lunch

    http://www.youtube.com/watch?v=pQ50PYMXDCQ

    ———

    It’s all in the numbers

    The Beauty of Mathematics and the Love of God!

    I bet you will NOT be able to read it without sending it on or telling at least one other person!

    Beauty of Mathematics!!!!!!!
    It was always fun to wow students via principles of 8 & 9:
    1 x 8 + 1 = 9
    12 x 8 + 2 = 98
    123 x 8 + 3 = 987
    1234 x 8 + 4 = 9876
    12345 x 8 + 5 = 98765
    123456 x 8 + 6 = 987654
    1234567 x 8 + 7 = 9876543
    12345678 x 8 + 8 = 98765432
    123456789 x 8 + 9 = 987654321

    0 x 9 + 1 = 1
    1 x 9 + 2 = 11
    12 x 9 + 3 = 111
    123 x 9 + 4 = 1111
    1234 x 9 + 5 = 11111
    12345 x 9 + 6 = 111111
    123456 x 9 + 7 = 1111111
    1234567 x 9 + 8 = 11111111
    12345678 x 9 + 9 = 111111111
    123456789 x 9 +10= 1111111111

    9 x 9 + 7 = 88
    98 x 9 + 6 = 888
    987 x 9 + 5 = 8888
    9876 x 9 + 4 = 88888
    98765 x 9 + 3 = 888888
    987654 x 9 + 2 = 8888888
    9876543 x 9 + 1 = 88888888
    98765432 x 9 + 0 = 888888888

    Brilliant, isn’t it?

    And look at this symmetry:

    1 x 1 = 1
    11 x 11 = 121
    111 x 111 = 12321
    1111 x 1111 = 1234321
    11111 x 11111 = 123454321
    111111 x 111111 = 12345654321
    1111111 x 1111111 = 1234567654321
    11111111 x 11111111 = 123456787654321
    111111111 x 111111111 = 12345678987654321

    Mind Boggling…

    Now, take a look at this…

    101%

    >From a strictly mathematical viewpoint:

    What Equals 100%?

    What does it mean to give MORE than 100%?

    Ever wonder about those people who say they
    are giving more than 100%?

    We have all been in situations where someone wants you to

    GIVE OVER 100%…

    How about ACHIEVING 101%?

    What equals 100% in life?

    Here’s a little mathematical formula that might help
    answer these questions:

    If:

    A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

    Is represented as:

    1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26.

    Then:

    H-A-R-D-W-O- R- K

    8+1+18+4+23+15+18+11 = 98%

    And:

    K-N-O-W-L-E- D-G-E

    11+14+15+23+12+5+4+7+ 5 = 96%

    But:

    A-T-T-I-T-U- D-E

    1+20+20+9+20+ 21+4+5 = 100%

    THEN, look how far the love of God will take you:

    L-O-V-E-O-F- G-O-D
    12+15+22+5+15+ 6+7+15+4 = 101%

    Therefore, one can conclude with mathematical certainty that:

    While Hard Work and Knowledge will get you close, and Attitude will
    get you there, It’s the Love of God that will put you over the top!

    Have a nice day & God bless you

  245. CJYman:
    “Furthermore, I can also show that events known to have required foresight in their construction are definable in terms of organized CSI.”

    Mustela:
    “I would like to see that calculation.”

    Excellent. Let’s look at an oil refinery, courtesy of wikipedia:
    http://en.wikipedia.org/wiki/Oil_refinery

    Let’s begin with defining the connections between each “unit” in the diagram in terms of CSI.

    We have 20 “units” or stations which can be connected in any way, since there is no regularity in the connections which can be defined by mathematical formula, and the connections themselves are not attracted to any specific station at the exclusion of the others through the physical properties of either the connectors or the stations. So, we can eliminate law and as long as the pattern is indeed not random, then we can say it is organized.

    We are definitely looking at a specified event, since f(pattern of connections and specific stations)= functional event of a usable product. So, yes the pattern is functionally organized. If we can calculate a > 1 value for CSI, the oil refinery would be an example of FSCI.

    Please excuse any small math errors as I am going through this relatively quickly.

    So, there are 20 units, and thus approx 1.57 * 10^57 possible ways of connecting them.

    Thus P(T|H) = 1/(1.57*10^57)

    In order to calculate the specificity, we need to know, utilizing the same stations, how many possible combinations of connections will also produce a usable product. This is where feedback from a professional would be useful. However, if this is a very specific configuration, and any improper connection will shut down the process …

    then S(t) = 1

    Now, we could use 10^120 as our probabilistic resources, but to get a more accurate calculation we should take into consideration what would be necessary for this plant to operate in space. Would more components be required? If so, then our calculation of probabilistic resources should take into consideration that this configuration could only operate on certain planets. After calculating this, which I will provide as an estimate when I have some time to research the variables, we will arrive at an accurate value for the probabilistic resources.

    Then, put it together:
    CSI = -log2[M*N*s(T)*P(T|H), and we have the connection specified complexity.

    But, there would of course be more to do. We need to figure out the CSI of every station/unit utilizing the above approach and then combine that value with the connection specified complexity to finally arrive at the CSI of the oil refinery depicted at the wikipedia link.

    For whomever is interested, go ahead and do some research and make the calculations. I will do the same when and if I have time and we can compare results.

    For now, though, I have shown that it is definitely theoretically possible to get a lower limit at least on the amount of CSI present in the above configuration. And I have already previously calculated a lower limit of CSI for the protein Titin in a likewise manner to show that it is indeed possible to do so.

    So there you have it — an explanation, with some preliminary calculation showing that an oil refinery (which definitely requires foresight on the part of engineers) is definable in terms of organized CSI.

    As a comparison, check out the schematic for this:
    http://www.sciencemusings.com/.....733633.jpg

  246. In fairness to the original post, most of the calculations here seem to take modern protein catalysts of many amino acids spontaneously developing. We might assume something with a minimal genome, or mimi-virus like as the original design. But what if it is even simpler? It might not even ‘look’ designed.

    For example, It has been shown short peptides and RNA are catalytic.

    I don’t think the CSI for a single proline or Val-Val dipeptide would be very high, yet they achieve remarkable catalysis and sterospecificity. It is possible that CSI started very low, and information was added with selection, energy, etc. over time.

    http://www.scripps.edu/newsand.....large.html

    http://www.pnas.org/content/103/34/12713.long

  247. 248

    CJYman at 244,

    “This isn’t my understanding from No Free Lunch, other papers, and other ID proponents on this site.”

    You expect everyone to have the exact same understanding?

    For such a core concept, one of the primary pieces of what is claimed to be positive evidence for ID, I definitely expect there to be agreement on the definition.

    You do realize not everyone understands or has the same hypothesis for evolution, right?

    There is ongoing research in numerous areas, but the core concepts of the theory are agreed upon and everyone uses the same definitions.

  248. 249

    CJYman at 244,

    I’m afraid that we’re discussing two different concepts. I’ll pick a few lines from your post to explain why I’ve come to this conclusion. Please let me know if you think my excerpts leave out relevant context.

    “When you say “chance hypothesis” do you mean “de novo creation”?”

    What else can you offer that utilizes only chance? Evolutionary algorithms sure don’t work only by chance.

    . . .

    CSI rules out chance very effectively

    . . .

    And yes, CSI does not take evolutionary mechanisms into account.

    . . .

    “We’re talking about evolution, not physics. I think I mentioned during one of our last discussions that you might be able to make a case for cosmological ID using the NFL theorems, but they are completely inapplicable when discussing the evolution that is observed in the one biosphere we know about.”

    I have been making a case for cosmological ID this whole time

    . . .

    “CSI is supposed to show that intelligent intervention is required for a particular biological artifact to exist.”

    I emphatically disagree!!!!!!! CSI requires no intervention as long as an evolutionary algorithm of any type can account for said pattern.

    . . .

    Simply, CSI provides evidence for evolution; it does not “rule out” evolution.

    . . .

    “…and changes in the length of a genome, for example, can be explained by known types of mutations.”

    And because they are “known types of mutations” means what exactly in light of calculating for CSI?

    It seems to me that your version of CSI is sufficiently different from that described by Dembski in No Free Lunch and in other papers as to be a completely different concept. Dembski’s CSI is supposed to demonstrate that intelligent intervention is required to explain how evolution occurred. It also is supposed to take into account known natural mechanisms; it is not merely a measurement of the probability of de novo creation.

    I’m looking to gain a better understanding of CSI as described by Dembski, since it seems to be one of the primary positive claims in support of ID. Your cosmological CSI approach is interesting, and frankly I suspect easier to defend both scientifically and theologically, but it doesn’t shed light on CSI as described in No Free Lunch.

    If you disagree or, even better, if you’d like to take a stab at a mathematically rigorous calculation of CSI, as described in No Free Lunch, for a real biological artifact, taking into consideration known physics, chemistry, and evolutionary mechanisms, I’d love to continue the discussion.

  249. Hello Mustela,

    Well, it seems we have come to the end of this road, and it has been a pleasure having this discussion with you.

    The measurement for CSI that I use is based on the most recent work on the subject by Dr. Dembski “Specifications: the Patterns which Signify Intelligence.” CSI can be measured at different points and with different givens … ie: from earth, given a full genome; or from our solar system, given nucleic acids; or our universe, given only matter and energy.

    No matter what the crowd states, and Dr. Dembski has explained this (I’m very sure I’ve read him explain somewhere) and I believe I have adequately explained above, there is no *requirement/necessity*, in the measurement for CSI itself as based on the equation given by DR. Dembski, for direct intervention — that is, unless evolution can be ruled out, but I see no way that one can rule out evolution for two reasons …

    1. the alternative, direct intervention, as it relates to the origin of CSI within our universe is about as useful as “last Thursdayism.” It may be true, but going as far back in time as we can until we get to the first CSI event, the only possible solution would be for a hand to “rip through space and time” and fashion the first instance of CSI. Is this scientifically useful? I vote, not at all!

    2. no matter the improbability, there is always a way to set up a program to generate an event. Look at a car factory and the robots assembling the car in stages. That’s all an EA really is … a program (robot) used to generate a highly improbable and specified event efficiently.

    … Oh, least I forget, there is another possibility … life has always existed in an infinite universe. But that is definitely for another discussion.

    Since I am by no means an “interventionist,” I will not be able to defend the “interventionist” position which is what you seem to be asking of me. In fact, I will help you argue against such a position as it pertains to life.

    All I have done (I believe effectively) is defend the position that CSI is indicative of previous intelligent causation — which is all that the equation for CSI, along with an understanding of organization, can tell us. Furthermore, that hypothesis has not yet been refuted through experimentation with computer simulation.

    The equation for CSI can’t tell us exactly “how” the artifact was generated — through evolution or through a robotic warehouse, or through direct intervention, etc. It merely, literally tells us in a mathematical form, that we are not dealing with a uniform probability distribution … that is it. Then, the NFL Theorems take over and the argument for CSI as a reliable indicator of previous intelligence continues, which I have briefly touched on above.

    So, I’m off to get me some more edumacation today, so I’ll be busy for the next couple days. I hope to hear from you again either in this thread or a future one.

    …later…

    PS. my position is somewhere in between/ a combination of Dr. Behe’s and Denton’s viewpoint.

  250. 251

    CJYman at 250,

    Well, it seems we have come to the end of this road, and it has been a pleasure having this discussion with you.

    And you as well. I appreciate you taking the time to present your remarkably nuanced view. I look forward to discussions on other topics here with you — perhaps we’ll even end up on the same side!

    Regards.

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