What has Gpuccio’s challenge shown?

(Sorry this is so long – I am in a hurry)

Gpuccio challenged myself and others to come up with examples of dFSCI which were not designed. Not surprisingly the result was that I thought I had produced examples and he thought I hadn’t.  At the risk of seeming obsessed with dFSCI I want assess what I (and hopefully others) learned from this exercise.

Lesson 1) dFSCI is not precisely defined.

This is for several reasons. Gpuccio defines dFSCI as:

“Any material object whose arrangement is such that a string of digital values can be read in it according to some code, and for which string of values a conscious observer can objectively define a function, objectively specifying a method to evaluate its presence or absence in any digital string of information, is said to be functionally specified (for that explaicit function).

The complexity (in bits) of the target space (the set of digital strings of the same or similar length that can effectively convey that function according to the definition), divided by the complexity in bits of the search space (the total nuber of strings of that length) is said to be the functional complexity of that string for that function.

Any string that exhibits functional complexity higher than some conventional threshold, that can be defined according to the system we are considering (500 bits is an UPB; 150 bits is, IMO, a reliable Biological Probability Bound, for reasons that I have discussed) is said to exhibit dFSCI. It is required also that no deterministic explanation for that string is known.”

(In some other definitions Gpuccio has also included the condition that the string should not be compressible)

These ambiguities emerged:

Some functions are not acceptable but it is not clear which ones.  In particular I believe that functions have to be prespecified(although Gpuccio would dispute this). Also functions which consist of identifying the content of  “data strings” (a term which is itself not so clear) are not acceptable because the string in question could have been created by copying the data string.

The phrase “no deterministic explanation for that string is known” is vague.  It is not clear in how much detail and how certainly the deterministic processes have to be known. For example, it appears from above the possibility that the string in question might have been copied from the string defining the function by some unknown method is sufficient to  count as a known deterministic explanation. This implies that really it is sufficient to be able to conceive of the very vague outlines of a determinist process to remove dFSCI. I think this amounts to another implicit condition: no causal relationship between the function and the string.

Lesson 2)  dFSCI is not a property of the string.

It is a relationship between a string, a function and an observer’s knowledge. Therefore, it may be that dFSCI applies for a string for one observer with a certain function but not for another observer with a different function.  The rules for deciding which function are not clear.

Lesson 3) The process for establishing the relationship 100% specificity of dFSCI and design is not commonly found outside examples created by people to test the process.

Gpuccio says thisabout the process:

“To assess the dFSCI procedure I have to “imagine” absolutely nothing. I have to assess dFSCI without knowing the origin, and then checking my assessment with the known origin.”

When challenged he was unable to name any instances of this happening outside the context of people creating or selecting strings to test the process as in our discussions. This is important as the dFSCI/design relationship is meant to be an empirical observation about the real world applicable to a broad range of circumstances (so that it can reasonably be extended to life). If it is only observed in the very special circumstances of people making up examples over the internet then the extension to life is not justifiable. To give a medical analogy. It might well be that a blood test for cancer gives 100% specificity for rats in laboratory conditions. This is not sufficient to have any faith in it working for rats in the wild, much less people in the wild. Below I discuss what is special about the examples created by people to test about the process.

A Suggested Simplification for dFSCI

dFSCI says that given an observer and a digital string where:

1) The observer can identify a function for that string

2) The string is complex in the sense that if you just created strings “at random” the chances of it performing the function are negligible

3) The string is not compressible

4) The observer knows of no known deterministic explanation for producing the string

Then in all such cases if the origin eventually becomes known it turns out to include design.

Given the rather lax conditions for “knowing of a deterministic mechanism” that emerged above, surely  (2) and (3) are  just special cases of (4). If (2) or (3) were present then deterministic mechanisms would be conceivable for creating strings.

So the dFSCI argument could be restated:

Given an observer and a digital string where:

* The observer can identify a function for that string

* The observer cannot conceive of a deterministic explanation for producing the string

Then in all such cases if the origin eventually becomes known it turns out to include design.

Conclusion

There are two main objections to the ID argument:

A) There are deterministic explanations for life.

B) Even if there were no deterministic explanations it would not follow that life was designed

For the purposes of this discussion I will pretend (A) is false and focus on (B)

No one disputes that it is possible to detect design.  The objectors to ID just believe that B) true. The correct way of detecting design is to compare a specific design hypothesis with alternatives and assess which is provides the best explanation. This includes assessing the possibility of the designer existing and having the motivation and ability to implement the design.   If no specific hypothesis is available then nothing can be inferred.

So is the dFSCI claim above true and if so does it provide a valid alternative way of detecting design?

The trouble is that there is dearth of such situations. One of the reasons for this is that digital strings do not exist in nature above the molecular level.  At any other level it is only a human interpretation that imposes a digital structure on analogue phenomena.  The characters you are reading on this screen are analogue marks on the screen. It is you that is categorising them into characters. So all such strings are created by human processes. It follows that design is a very plausible explanation for any such string.  People were involved in the creation and could easily have designed the string. If you add the conditions that the function must be prespecified and there should be no causal relationship between the function and the string then design is going to be by far the best explanation. It goes further than that.  It also means there almost no real situations where someone is confronted with a digital string without knowing quite a bit about its origin – which is presumably why Gpuccio can only point to examples created/selected by bloggers.

What about the molecular level?  Here there are digital strings that are not the result of human interpretation. Now human design is massively implausible (except for a few very exceptional cases).  The problem now is that carbon chains are the only digital strings with any kind of complexity and these are just the one’s we are trying to evaluate. There are no digital strings at the molecular level with dFSCI except for those involved in life.

So actually the dFSCI argument only applies to a very limited set of circumstances where a Bayesian inference would come to the same conclusion.

493 thoughts on “What has Gpuccio’s challenge shown?

  1. Joe: “Mt Everest did not exist in the pre-flood world. All the mountains and ocean basins were created during the flood year. That is if you actually know the flood story. “

    Joe, you seem to be saying you believe in the Ark story in every way but saying, “I believe in the Ark story”.

    Please tell me how we can take anyone seriously when it comes to science, if they actually believe that.

    Joe, do you believe in the Ark story as being literally true?

     

  2. Joe: “And Patrick responds to Elzinga’s strawman by acting like it reflects reality. “

    How does Mike Elzinga’s comment not reflect the reality of the physics problem of the Ark story?

     

  3. Patrick notes: Preserving their ability to believe in a global flood is just one of the reasons why it is so vital that they misunderstand thermodynamics.

    Indeed.

    One of the more common arguments they try to muster is that there were no oceans or mountains before the flood, thus no water depth.

    However, they don’t even know how to calculate how much energy is required to make the oceans and mountains; and as it turns out, those energies are even far larger than the energy of all that water coming down from outer space. Plowing up all that granite and digging those ocean depths requires far more energy than just dumping all that water on the Earth.

    It is the little things like these calculations that betray the self-imposed ignorance ID/creationists carefully maintain for themselves. It appears that they really believe that, by never learning any science, they are not responsible for checking anything out; and they can simply assert that scientists and high school students are liars whenever scientists and high school students can produce calculations that debunk creationist myths

    It is very peculiar phenomenon to watch; and I have observed it in nearly every ID/creationist I have encountered over a period of nearly 60 years. It happens every time; and they don’t even know what they are revealing about themselves when they sneer at the calculations and offer “reasons” why the calculations are wrong while trying to word-game them away.

  4. Joe: “Dude, buy a vowel- look what YOU believe in. That is why I will never take any evolutionist seriously when it comes to science. “

    But the ID side is asking a school board to look at ID as science, when those same proponents don’t know enough science to realize the Ark story cannot in any way literally be true.

    Joe, do you believe the Ark story is literally true?

     

  5. Joe: “Not quite. The ocean’s basins weren’t as deep as they are now and water would have been circulating under the continents. There it would get warmed up and when it came out it would help keep the earth nice and warm. “

    Nice and warm???

    We are talking major heat wave! 🙂

    Joe, please, do you believe in a literal Ark story, yes or no?

     

  6. Joe. It would help your case if you could actually give some citations or thoughts as to why you think Mike’s case is “a straw man” or how you or other YECs think it could have happened. Thanks!

  7. I watched the video – so much wrong! but I’d like to know why the lakes that were left aren’t saltwater, but the seas are?

  8. Joe – Mike’s offered an analysis based on physics.

    You’ve offered a story from the bible.

    But ID isn’t religious.    

  9. Joe, do you not think that the ark story is a part of a bigger ID narrative, bilbical creationism?

  10. I heard Walter T. Brown debate a biologist in Rochester, NY back in February 1, 1986; and I have read much of what Brown has written.

    Back in 1986, Duane Gish, Henry Morris, and Walter Brown were bashing biologists with the “evolution violates the second law of thermodynamics” argument.  I was stunned at how stupid Brown was on the second law, but he bamboozled the biologist at the time.

    Brown supposedly has a PhD in mechanical engineering from MIT.  It just goes to show that PhDs among creationists don’t mean anything.  They either didn’t really learn the stuff, or they are deliberately getting it wrong in order to taunt scientists into debates with them.

    I am pretty sure that the taunting had a lot to do with it.  That is how the creationists leveraged “legitimacy” from the scientific community back then; they rode on the backs of scientists in highly publicized debates and just threw crap all over the place in order to aggravate their opponents.  That was before the scientific community caught on to the tactic and stopped giving creationists a free ride.

     

  11. Pssssst, Joe:

    http://www.conservapedia.com/Baraminology

    “Baraminology, as a model of origins, complements the Linnaean taxonomic system, which is also based on the Biblical view of origins. ”

    ” An example would be dogs, which form a holobaramin since wolves, coyotes, domesticated dogs and other canids are all descended from two individuals taken aboard the Ark, and there are no other creatures that are genetically continuous with them. This term is synonymous with the use of “baramin” above and is the primary term in baraminology. “

  12. Joe: “don’t blame me because the evidence supports baraminology”

    Baraminology: “based on the Biblical view of origins”

    Are you following the evidence where it leads, Joe?

  13. Toronto:You’re making “unguided evolution” sound powerful enough to alter body plans.

    Mung: What is ‘unguided evolution’ and how do you distinguish it from ‘not-unguided evolution’?”

    That’s gpuccio’s gig! 🙂

    While I have your attention, do you believe a literal Ark story is supported by science?

     

  14. Mung: I believe science supports the literal resurrection of Jesus Christ from the dead.

    If Jesus was literally raised from the dead, then what difference does the answer to your question make?

    But to answer you, I don’t think science addresses itself to whether the account of ‘Noah’s Ark’ in Genesis is ‘literally true’ or not.

    I’m one of those people that understands that many things in the Bible are not meant to be taken ‘literally’. Does that mean that the Bible is false? Hardly.

    As an atheist, the Bible makes a lot of sense to me only when it is taken in a non-literal way.

    The problem arises when Bible supporters insist on changing reality to support the Bible.

    This evolution debate pits literal interpretations of the Bible against science.

    So just to be sure I have it right, you do not believe in a literal Noah’s Ark story as portrayed in the Bible.

    Am I correct?

     

  15. Gpuccio,

    As promised, a Zachriel-style example of phylogenetic inference. Suppose you are told that strings 2 through 16 below are all descendants of a common ancestor, which is string 1 (the string with all commas). Try to reconstruct the tree, and think about the criteria you employ while doing so.

    Sorry about the spacing. WordPress isn’t allowing me to specify a monospaced font. If you copy and paste the strings into an editor that’s using a monospaced font, they’ll be easier to read and line up.

    1) ,,,,,,,,,,,,

    2) X,C,,,V,,,,P

     3) ,,,,J,,,OEQ,

     4) X,C,,,,,,,,P

     5) ,,,,J,,,OE,,

     6) ,,C,,,,,K,,,

     7) X,C,,,,,M,,P

     8) ,,C,,,,,,,,,

     9) X,,,,,R,,,,P

    10) ,,,,,,,,OE,,

    11) XUC,,,V,,,TP

    12) X,,,,,,,,,,,

    13) ,,,,J,,,,EQ,

    14) X,C,,,V,,,TP

    15) ,,C,,,,,KN,,

    16) X,,,,,,,,,,P

  16. Guys

    We seem to be drifting off-topic and away from Lizzie’s intention that thread comments should avoid personal attacks.

    The sandbox is there and there is the option of a new thread. 

  17. I believe he sometimes is only thinking within the scope of testing “dFSCI” as a design detection tool on known samples, but the way he is doing that is impacting on the possible real-world use of “dFSCI”

    I am sure gpuccio is only ever thinking in terms of known samples and is convinced that unexplored protein sequence space is a barren desert. What I don’t see is any justification for such a view.

  18. Brown’s PhD is real and earned. But it just goes to show that even a smart and educated person can go ’round the bend.

  19. Mung: GA’s are “EXHIBIT A” in the case for ID.

    We welcome the GA as evidence in our favor.

    All successful Biblical prophecies are evidence that humans don’t have free will, since there is no decision we can make that will stop them from happening.

    GA’s on the other hand, are tools, just like hammers, and trust me, what I build with a hammer, is never ever the result of design. 🙂

     

     

     

  20. Mung has many strong opinions:

    Joe Felsenstein on November 27, 2012 at 1:48 pm said:

    Joe F, if you see this,

    You seem to believe that natural selection increases combinatorial opportunities. I say that by whatever measure natural selection increases combinatorial opportunities it likewise decreases combinatorial opportunities.

    comment-440105

    And you say?

    I say that the original question was whether natural selection can put SI (and CSI) into the genome. Note the word “can”.

    Mung (#613) had responded that

    1. Natural selection doesn’t “put things into the genome.” At best it can only preserve or eliminate what is already there. For something to be “selectable” it must already exist.

    Natural selection can raise the frequency of rare alleles at two loci and make those frequencies high enough to allow the haplotype that has both of these alleles to exist in the population (formed by recombination). At their previous low frequencies the two alleles would not have existed in the same haplotype.

    Take a population of one million mosquitos. If allele A ot one locus has a gene frequency of 0.0001, and allele B at another locus has a frequency of 0.0001 also, then if they are associated at random, the haplotype AB would basically not exist in the population, as it would have an expected frequency of 0.00000001. Now suppose that A and B are favorable. Each rises to a frequency of 0.01. Now recombination between these loci would create AB haplotypes at a frequency of 0.0001, which is high enough that they really would exist in the population.

    Of course natural selection can also decrease the frequencies of A and B (say, if they are deleterious). But the issue here is not whether natural selection always, or even typically, does this or that. The issue is whether natural selection can bring about a situation where new combinations of alleles come into existence.

    Can.

    That is what is needed to refute assertions that natural processes such as natural selection, random mating, and recombination cannot increase SI enough to make it CSI.

    Mung: Natural selection, we are asked to believe, skews the results and makes the utterly impossible merely improbable, yeah, quoth Chucky D., nigh certain! AMEN! PRAISE EVO!

    bee period ess period

    Faced with facts, evos are silent.

    The argument is above. Mung might try refuting it. Or Mung might try to address the more important issue by coming up with some logical argument as to why natural selection cannot shift gene frequencies enough to get us far enough out on the fitness scale for the change to constitute CSI. Hollering and insulting won’t do the job. We’re all waiting for the mathematical argument. And waiting, and waiting …

     

  21. You’re right Alan. I was just fascinated by Joe’s YEcism and attempted defense that the flood was a historic event.

  22. Mung

    You seem to believe that natural selection increases combinatorial opportunities. I say that by whatever measure natural selection increases combinatorial opportunities it likewise decreases combinatorial opportunities.

    Could Mung be mixing up the roles of natural selection and recombination?

    Recombination can indeed break AB combinations as well as form them, and in a completely selection-free world, there would be no reason for them to increase beyond chance (though there would also be no reason for us to think the combination in any way special, if it plays no part in an organism’s ‘fitness’ for its environment).

    If AB happens, the crossover that caused it both created AB, and created not-A/not-B in another gamete from the alleles. At that point, it’s symmetrical.

    A fresh AB is no different from a brand new mutation, except that ‘back-mutation’ is more likely by intervening crossover. If AB is fitter than other combinations of A, B and their alleles, NS would shift the balance, just as it would a mutation. The population will tend to shift towards increasing AB, which will remain unsevered in more meioses than break it assuming they are on the same chromosome. 

    AB individuals will have a proportion of A or B offspring, but this proportion will diminish as frequencies rise – as AB gains in frequency, so too will A and B, the non-AB offspring of AB/’wild-type’ crosses. A and B alone hitch a ride on AB’s fitness. In such a population, with AB, A and B now at significant frequency, AB recombinations will happen more often, while AB-breaking recombinations would be less likely, since even when crossover occurs between them the recombinational partner is likely to be another AB (no difference), or A or B alone (no difference 50% of the time). Eventually, when AB is fixed, neither recombination nor selection can do any work on it. But on the way there, they both play a part in ‘putting’ AB into the genome of the future population, ready for someone to come along, pick an individual and say “AB! I wonder how that got there?”..

  23. gpuccio: You seem to have a hard time with truth. Where did I say such things? Please, show.

    a) dFSCI is something that a string exhibits, and we can recognize. The judgement about the dFSCI if a string, if correctly given, remains the same.

    b) There is no need to know how the string was generated to assess dFSCI for it. It is necessary, however, to define explicitly a function for it, and to know something of the System and Time span where the string emerged, essentially to compute the probabilistic resources of the System and to choose an appropriate threshold for dFSCI in that context. As I have said many times, always in the same way.

    But you said this previously:

    gpuccio: The correct version:

    1a) gpuccio observes that the strin X has a function and explicitly defines it.

    1b) gpuccio computes the functional information for that function, and observes that it is high, higher than an appropriate threshold for the System and the Time Span.

    1c) after careful observation and consideration, gpuccio isn’t aware of a ‘necessity mechanism’ that explains X to his satisfaction;

    2) therefore X exhibits dFSCI;

    At 1b), you have all the attributes required to attribute “dFSCI” except, how this string came to be in this configuration.

    At 1c), you check how this string came to be in this configuration.

    At 2), after ruling out some reasons of how this string configuration came about, e.g. a “necessity mechanism”, you then attribute “dFSCI”.

    Please tell me why I should not be confused.

    All you had to do to be consistent in both test situations and real-life use of “dFSCI”, is to assess “dFSCI” regardless of how that string came to be, and then, after that, assess positive_for_design if you thought the string required an intelligent agent.

    That’s all, just use terminology that is clear.

    All confusion would have have been avoided, your argument would have been unchanged, your conclusions would have been unchanged, and there would have been no need for you to call many of us liars.

     

  24. gpuccio: I count on no extra information. I am only waiting that you stop talking, and deliver.

    1.0) You will get a string of 500 bits or more that is functional software, i.e. x86 machine code that will perform some functions that no one has any prior knowledge of.

    If I generate such a string, which is unknown to anyone including me, is this enough to invalidate “dFSCI” as a design detection tool?

     

     

  25. GP, to Alan Fox:

    The 2000 superfamilies are completely isolated one from the other at sequence level and strucutre level. This is a very simple fact, that can be easily verified by the BLAST tool, as I have showed.

    b) You may think that those 2000 functional islands are possibly joined by functional “bridges” in the protein space. That would be absolutely critical for the neo darwinian theory to be even remotely credible.

    c) But remember, those “bridges” should be made of naturally selectable sequences, each with increasing function. That is the only “function” that makes sense for the neo darwinian algorithm.

    This just isn’t true. It isn’t essential – nor even plausible –  that every step in a protein’s history should be fixed in a population by natural selection. Those that were were fixed according to the selective forces in operation at that particular point in history – which includes the other alleles in the population, and the other genes in the genome. All lost history. Nonetheless, this hardly invalidates ‘neo-Darwinism’ and common descent as a source of all such sequences, any more than the lack of relationship between – say – Basque and other languages forces us to conclude that they were  developed entirely separately from basic grunts.

    GP is essentially declaring that the superfamilies are islanded because sequence/structure commonality hasn’t just been obliterated by time, it never existed. His evidence for that non-existence is that no-one can reconstruct the particular changes in sequence or show the benefit accruing to the unknown organism in which it occurred.

    The argument is fundamentally preposterous – show me the intermediates, which we all know are dead and gone, or I must invoke a Designer, operating by unknown means on unknown elements of the sequence for unknown reasons at unknown points in history – that’s a superior explanation!

    Consider a sequence of 1000 amino acids possessed by two isolated populations with initially 100% commonality by descent. At random, substitute 1 acid every 500,000 years. How much sequence commonality would be expected to remain after 1 billion Years? Of course, GP is convinced that proteins are islanded, so he cannot conceive of such extensive substitutions taking place. But the evidence is not on his side – libraries of proteins constructed randomly are found to have a variety of functions, acid-by-acid substitutions have found proteins to be extremely tolerant of considerable change, even without duplication. On empirical evidence, proteins are not islanded. A lack of commonality of both sequence and structure is not sufficient to conclude that proteins MUST be unrelated unless someone shows the steps. Once the signal of descent is obliterated, one has of course no surviving evidence that they are.

  26. gpuccio (in #783):

    I fully agree that any genome, or other informational structure, can increase
    in SI by RV and intelligent selection. That is true, and easily attained.

    (quoting me): The question being addressed was whether there was some general proof that models of genomes that had mutation, natural selection, and recombination could not put SI (and CSI) into the genome.

    OK, so once again it all hinges on when selection is “natural”.  If we set up an computer model with fitnesses, genotypes, mutations, recombination, then the fitnesses must meet gpuccio’s standards to have the simulation accepted. Just showing that there are (many sets of) fitnesses that can lead to SI increasing, and CSI coming to be present, is not enough. For then gpuccio will declare that we have made a case of “intelligent selection” but not “natural selection”.

    I will readily acknowledge that I have made no big distinction between “selection” and “natural selection” in my posts here. I just am not as sure as gpuccio is how to distinguish between natural and unnatural fitnesses.

    [gpuccio quoting me]: I guess that if gpuccio has such a proof, or if Dr. Dembski has such a proof, the genetic systems and selection regimes that their proof applies to do not include the model that I presented. Anyway I have not seen any proof from them.

    [gouccio]: Not only I have not any proof of that. I have said a lot of times that RV + Intelligent selection can generate new dFSCI. And that RV + NS cannot do that.

    It is worse than that: gpuccio has presented no logical argument or mathematical theorem, or even computer model to back up the assertion that “RV+NS cannot do that”. For Dembski’s CSI, there is also no argument or theorem, Dembski’s proposed ones having collapsed. So all the posters and commenters at UD who keep saying that RV+NS cannot lead to CSI being in the genome are standing on thin air.
     

    As I have given proof that you have intentionally changed “the question being addressed” in your post.

    See above. I am happy to restrict the questions to “natural” selection if gpuccio and I can agree what is “natural”. Dembski’s attempted proofs did not attempt that, but instead presented a theorem (his Law of Conservation of Complex Specified Information) that applied to all sets of fitnesses. Thus if true it would definitely apply to “natural” fitnesses.

    Skipping other issues which we can come back to if they are important enough — I do have answers for those — I note that gpuccio does define what the distinction is between “natural” and “intelligent” selection:

    NS is that kind of selection (more correctly, effect) that can happen in a System where there are replicators interacting with environmental resource, and that is due only to the reproductive advantage that some kind of replicator can acquire.

    Intelligent selection is any kind of selection where a conscious intelligent being decides what to select, and what the effects of selection will be.

    Simple, isn’t it? NS is “natural” in the sense that it needs no intervention of a designer (once the System with the replicators is already set).

    OK, so if I make an evolutionary algorithm with genotypes that lead to phenotypes, and these phenotypes have different abilities to get resources, and the reproduction depends on how much resources each individual can get, gpuccio will say “OK, that is natural selection. Now let’s see what it can or can’t do”? Why do I worry that no matter how I do that, gpuccio will say that no, that way of getting phenotypes from genotypes is not natural, but is intelligently designed by me, and that rule for which phenotype gets which amount of resources is not natural, but is intelligently designed by me.

    Perhaps gpuccio could demonstrate that this would not be a futile exercise by having gpuccio set up the model. Then we could see whether it can be shown that the model cannot out some appropriate form of SI into the genome.

  27. I posted some very simple output histories from a simple GA the demonstrate the obliteration of history. This is why gpuccio will not allow GAs as a model of evolution. They obliterate the mathematical basis for his argument.

  28. keiths:

    As promised, a Zachriel-style example of phylogenetic inference. Suppose you are told that strings 2 through 16 below are all descendants of a common ancestor, which is string 1 (the string with all commas). Try to reconstruct the tree, and think about the criteria you employ while doing so.

    gpuccio:

    Excuse me, I have no time for that.

    I see. You have time to post 2,000+ words a day, on average, but you can’t spare a few minutes to work through a simple exercise in phylogenetic inference.

    That’s a pity, especially considering that the entire issue right now is your misunderstanding of the prerequisites for successful phylogenetic inferences.

    What I expect from you is that you show me how that is relevant for true biological hierarchies, and where that makes a difference with a design explanation. Please, stick to that.

    Okay, since your time is so much more valuable than mine, here’s an example of how design gets in the way of successful phylogenetic inferences.

    Suppose we are looking at the genomes of a large, varied group of organisms. We notice that 25 of them share a particular, very complicated set of identical genes, which we’ll call B. When we are trying to reconstruct the phylogeny of the entire group, which of the following assumptions is the most rational one for us to make?

    1. Assume that B was present in the common ancestor of all 25 of the organisms that now have it.

    2. Assume that B arose independently in all 25 organisms, and that it just happens to be identical in all 25.

    3. Assume something in between, where B arose independently (and identically) in more than one lineage, each of which passed it down to its descendants.

    The answer, of course, is #1. B is a complicated set of genes, so the odds of it arising independently and identically in multiple lineages is vanishingly small. It is much more likely that B was present in the common ancestor and was passed down to all the descendants.

    Now suppose that instead of organisms we are talking about different models sold by a computer company. The models vary in terms of the processor chip, the amount and speed of memory, the size and speed of the hard drive, etc. Let’s say the company has been selling these models for a while when Blu-ray drives first become available. The company takes 25 of its existing models and creates new models by adding a Blu-ray drive to each of them.

    Now, if we are trying to infer the “phylogeny” of these computer models, having no knowledge of how they actually evolved, can we assume that the Blu-ray drive was present in the “common ancestor” of all 25 of the models that now have it? No, of course not. It might have been there, or it might not (in reality, it was not — but we don’t know that). Computers are designed, and so both of those scenarios are possible.

    Here’s the key point:  The assumptions that allow us to infer phylogenies successfully when classifying living organisms don’t work when applied to designed objects (unless the designer mimics evolution, of course). As the Blu-ray example shows, we won’t get the same hierarchy when looking at two different sets of traits.  To use Theobald’s terminology, the hierarchies are subjective in the case of design.

    Under the design hypothesis — including those forms that admit common descent — we have no reason to expect the hierarchies to match, much less match perfectly. Yet the theory of unguided evolution gets it exactly right in the case of Theobald’s 30 taxa. The inferred hierarchies match perfectly, even though there are 1038 ways for them to mismatch.  Unguided evolution predicts that we will see an objective nested hierarchy, and the prediction is confirmed in spectacular fashion.  

    The rational conclusion is that unguided evolution explains the evidence far better than ID. The race is not even close. Evolution is a better theory.

  29. Joe Felsenstein:

    I am happy to restrict the questions to “natural” selection if gpuccio and I can agree what is “natural”…

    I note that gpuccio does define what the distinction is between “natural” and “intelligent” selection:

    NS is that kind of selection (more correctly, effect) that can happen in a System where there are replicators interacting with environmental resource, and that is due only to the reproductive advantage that some kind of replicator can acquire.

    Intelligent selection is any kind of selection where a conscious intelligent being decides what to select, and what the effects of selection will be.

    Simple, isn’t it? NS is “natural” in the sense that it needs no intervention of a designer (once the System with the replicators is already set).

    OK, so if I make an evolutionary algorithm with genotypes that lead to phenotypes, and these phenotypes have different abilities to get resources, and the reproduction depends on how much resources each individual can get, gpuccio will say “OK, that is natural selection. Now let’s see what it can or can’t do”? Why do I worry that no matter how I do that, gpuccio will say that no, that way of getting phenotypes from genotypes is not natural, but is intelligently designed by me, and that rule for which phenotype gets which amount of resources is not natural, but is intelligently designed by me.

    Joe, I think your worry is well founded. Gpuccio, like many ID proponents, seems to chronically confuse the model with the thing being modeled.

    In a model of Darwinian evolution, we model variation, we model replication, and we model selection. The fact that the models are designed is a given, but it has no bearing on whether the processes being modeled are natural or artificial.

    This is obvious in other contexts. A computer model of rainfall patterns is designed, but nobody would contend that the rainfall being modeled is therefore “intelligent rainfall”. Yet gpuccio seems to think that a designed model of natural selection is necessarily, by virtue of being designed, a model of ‘intelligent selection’.

    I’ve gone over this with him before, and I thought he was starting to get it, but other things he’s said since then seem to indicate otherwise.

  30. GP: each with increasing function.

    Petrushka: Untrue.

    Er, yes – a somewhat more succinct statement of my opening argument! This is the version of evolution attacked by many of the highly-educated critics – Spetner, etc. Every incremental change must have phenotypic effect and be favoured by NS, a highly improbable state-of-affairs. I do wish they’d get to grips with the theory before tilting at it.

  31. I’ve gone over this with him before, and I thought he was starting to get it, but other things he’s said since then seem to indicate otherwise.

    He’ll never get it as his entire argument depends on him not getting it. The answer is, as suggested, to get him to create a model that satisfies his own criteria. No doubt he’ll “not have time” for that either, preferring instead to write another 2000 word post that sidesteps the lack of an objective measure for dFSCI.

  32. gpuccio now seems willing to accept a model whose fitnesses depend on processing of “resources” in a “natural” way. But earlier gpuccio’s argument was the one you descirbe and was different — it was that since the model was designed that this means that the dFCSI is already present. (Kairosfocus has echoed that in their thread very recently).

    If gpuccio were to do the unexpected and actually come forth with a model which would show the ineffectiveness of NS in putting dFCSI into the genome, then do we expect gpuccio to raise the earlier criticism against gpuccio’s own model? It is a puzzle.

    Also, I expect that when (and if) it is clarified what patterns of fitnesses are “natural” to gpuccio, that the basic argument will be seen to be a version of Michael Behe’s argument, clothed in informationy language. 

  33. To everyone,

    Joe: Apologies KF, I am just telling the truth

    But yes, enough is enough- I just don’t like being lied to and about and it seems that is all “they” have.

    I am sure that you have noticed it too.

    What I have noticed from this whole gpuccio challenge is that UD is getting the benefit of not having to address everything the “banned”, like myself, have “corrected” IDists on.

    Joe, kairosfocus, Mung, gpuccio and Upright BiPed, have been able to call us liars and get away with it as far as readers of UD can see.

    Given that, I will only address comments made by ID/creationists on this blog.

    I also won’t read anything on UD anymore either, since the added traffic/visits will only be to their benefit, not mine since I am “banned” from participating.

    I won’t come back either even if my bannination is revoked since that would just increase UD’s traffic and not this one.

    So to all, think about only replying to comments posted here and let’s see if we can increase the traffic to this site.

    I somehow think they need us more than they let on. 🙂

  34. Joe, kairosfocus, Mung, gpuccio and Upright BiPed, have been able to call us liars and get away with it as far as readers of UD can see.

    That can be solved simply by not visiting their site.

    We have a couple of members her who report back on what they are saying.

    I only pay attention if they present some new argument, and so far that hasn’t happened.

  35. It has been becoming more and more obvious that there is another central, unifying theme running through “scientific” creationism and “intelligent” design (ID/creationism).

    Ken Ham has been doubling down and tripling down on this notion of “historical” science versus “operational” science (Ham doesn’t appear to know about basic science versus applied science and engineering).

    If one reads one of the more recent comments on this over on AiG, all it boils down to is “Ken Ham’s sectarian dogma must come first, and everything else must be bent and broken to fit.” One must read the Christian bible as Ken Ham reads it.

    The ID movement, besides picking up all their misconceptions and misrepresentations of energy and matter from the Henry Morris and Duane Gish, is constantly accusing the science community of the SIN of “materialism;” in other words, religious heresy.

    They simply cannot hide fact that this is all about establishing a sectarian hegemony; they conveniently keep forgetting their Wedge Document. Anyone who doesn’t follow their narrow sectarian dogma is accused of some kind of sin or heresy. You must accept sectarian dogma or you are damned.

    Yet not one of these ID/creationist pushers can get the science right even at the high school level. Their repeated, huge dumps of copy/paste, quote-mined material is designed to give the illusion of erudition and deep knowledge; but none of them can do even an elementary calculation involving high school knowledge of science. Even if someone does it for them, they still don’t know what any of it means.

    They have to have a canned, copy/paste response; and without it, they are helpless.

    I gather from Toronto’s observation that the traffic over at UD has picked up because of comments here. I don’t know if others are having the problem, but loading pages at UD locks up my computer for long periods of time. I stopped trying to follow the responses.

    They don’t deserve the traffic they are getting as a result of what people discuss here. They can’t respond in any coherent manner simply because they don’t have the copy/paste material at their fingertips.

    So apparently, judging from the comments I am seeing here, they are just dodging and sneering at everything.

    I thought the conversations here were more interesting when folks were ripping apart the “intellectual” works of the ID/creationist gurus. That level of discussion is too far above the level at which the crowd over at UD can handle because there are no copy/paste responses they can give to things that require real knowledge on their part.

    I recall the condescending sneers of some of those UD people who showed up here; yet they couldn’t answer anything once folks here got down to business. The UD people just couldn’t follow; and they had no copy/paste material they could use to give the appearance of understanding. All they could do is start making up crap and “new” theories in order to keep attention focused on themselves; and it never converges to anything.

    But that is the nature of ID/creationism; it can’t converge.

  36. Joe F:

    gpuccio now seems willing to accept a model whose fitnesses depend on processing of “resources” in a “natural” way.

    At one point, he did retract his claim that fitness functions are verboten:

    To onlooker (at TSZ):

    Any fitness function in any GA is intelligent selection, and in no way it models NS.

    Please, do not consider any more that statement. Keiths is right, it was a wrong generalization.

    But he’s still saying things like the following, which makes me wonder if he isn’t regressing to his earlier position:

    Intelligent selection is any kind of selection where a conscious intelligent being decides what to select, and what the effects of selection will be.

    In the case of a GA or a computational evolutionary model, the programmer makes those decisions. So according to gpuccio’s criterion, any such GA or model necessarily involves intelligent selection, not natural selection.

    It looks like he’s still confused.

  37. Patrick said: Yes! One more convert to the “screw the lid on tight and let them asphyxiate in their echo chamber” movement!

    That is indeed the position I have held for quite a few years now; let them asphyxiate in their own vapors. Studying them, their misconceptions, their misrepresentations, and their tactics is fine; but put the bulk of one’s time into educating students and the public about the ID/creationist scams and abuses of science.

    As is the case with nearly all pseudo-scientists, ID/creationists have always been insanely jealous of scientists and cloyingly desperate for free, public rides on the backs of high-profile scientists. We finally figured that out back in about the late 1980s and stopped giving them that ride.

    We also need to stop giving them feedback of any kind because they abuse every piece of information they are ever given and use it to become even more deceptive.

  38. The logic of all the above comments would be that people would advocate closing down TSZ.  I don’t think it should close down — people who don’t know how to evaluate ID arguments would then have nowhere to hear our voices.

    OK, I sense the frustration and anger, but … really close TSZ down? I vote no. 

  39. I hope I didn’t come across as thinking that TSZ should be closed down; I don’t.  There have been some really good discussions here; and I have really enjoyed them.

    It seems pretty clear however that the UD people are incapable of participating; and I for one would not help them out with anything.  The few times I have recently done so I have simply confirmed that I should not have.  I just end up repeating the lessons I learned about ID/creationists years ago.

  40. Joe F.:

    The logic of all the above comments would be that people would advocate closing down TSZ. I don’t think it should close down — people who don’t know how to evaluate ID arguments would then have nowhere to hear our voices.

    Joe,

    I don’t think they’re suggesting that TSZ should be shut down. They just want us to stop interacting with the folks at UD, as we have been in this thread and many others.

    Personally, I think that interacting with the UDers does more good than harm.

    1. Anyone stumbling onto our odd interblog conversation quickly figures out the reason for it: censorship and banning on the UD side. We welcome open discussion at TSZ. They don’t at UD. That immediately discredits UD in the eyes of any objective observer.

    2. IDers like to complain that their ideas aren’t given a fair hearing. TSZ puts the lie to that assertion. We go to great lengths to understand their claims, even when they don’t want us to (hi, Upright!). Look at how many threads we’ve dedicated to gpuccio’s argument, how much time we’ve spent parsing his very unclear declarations, and how much feedback we’ve given him.

    3. There are quite a few people who find pro-ID arguments persuasive in isolation. It’s good for such people to see that we can easily rebut those arguments and show that the evidence favors evolution over ID.

    4. Being called a liar by the likes of Mung or Joe is harmless. No one takes them seriously on either side of the debate.

    5. Interacting with the IDers reveals a lot about how they think, and why they make the mistakes they do. I think it’s fascinating and entertaining. It also suggests ways of better explaining evolution to those who don’t understand it.

    6. It gives us practice in expressing our positions clearly and logically to a hostile audience. That’s a useful skill to hone, even if the audience in this case tends to be impervious to reasoned argument.

  41. I’m certainly not suggesting that TSZ and similar sites be shut down.  I very much enjoy the posts by the regulars here and learn a great deal from all of you.

    I do believe that carrying on a discussion in such close parallel with that on UD implicitly sanctions their censorious moderation policies.  As something of a free speech absolutist, I find that immoral.  I am personally more than happy, eager even, to discuss intelligent design creationism in an open forum such as this one.  However, if the UD regulars lack the minimal intellectual courage to venture out of their cesspool, I don’t believe they deserve a direct response.

    TSZ and similar fora are an unfortunate necessity so long as IDers and other creationists threaten science education in this country.  The silver lining is that the science education many of you are providing has significant value after these hopefully transient death throes of fundamentalist religion subside.
     

  42. As someone who has been watching up close the tactics of ID/creationists since the 1970s, I don’t see much value in trying to discuss anything directly with them.

    For example, I still remember very clearly a debate I saw February 1, 1986 at Xerox Auditorium in Rochester, NY, between Walter T. Brown and a professor of Geology at SUNY Brockport.

    Brown came in sporting his credentials, with a PhD in mechanical engineering from MIT (where he was a National Science Foundation Fellow), full colonel in the Air Force, Associate Professor at the Air War Collage, Associate Professor at the US Air Force Academy, Director of Benet Research Engineering and Development Laboratory.

    I still have my detailed notes from that debate in which Brown, portraying himself as an expert in thermodynamics, bamboozled the crowd and won the debate.

    What I remember of that debate, and what is in my notes, is how absolutely atrociousness was Brown’s understanding of science, physics, and thermodynamics in particular.  This is the way of the ID/creationist; and it cannot be dealt with in debates.

    (Brown was one of the creationists that came up with a bamboozle story of the Flood; and he provided no evidence, nor did he ever calculate the energies involved in such rearrangement of the Earth’s surface.  He just hand-waved it.)

    What I had learned even before then – from having the records of earlier debates by Gish, Morris, and others – is that it is far better to study the misconceptions and tactics used by ID/creationists and to use them to find better ways to teach subject matter to students and the public.

    Misconceptions happen all the time; and educators become familiar with them and learn ways to deal with them.  However, until the formalization of “scientific” creationism and its morph into ID, there has not been in the history of the US, as far as I know, such a direct and deliberate assault on reason and science that has been hell bent on sewing confusion in order to advance sectarian ideology.

    That formal beginning started a set of well-funded institutions, the specific intent of which was for people to work full time spreading misinformation and confusion about science.  One of the worst parts of that war on science has been the generation of ready-to-fling feces of misinformation that requires no thinking on the part of the feces flingers.  It’s what they now do; nothing else.  They want the attention in order to get that crap out there.

    However, once you realize that the people flinging this crap don’t even have a high school level of understanding of science,; once you have seen “PhDs” flinging absolute crap while waving “impressive credentials,” you begin to realize that it is not just the science community, but the general public as well that is under a well-organized and coordinated attack.

    By engaging the attackers, you encourage the release of more toxic misinformation that is simply made up on the spot.  You need to learn the basic science and to teach the basic science and to inoculate the public.  You don’t do it by giving free rides to the perpetrators of ID/creationist crap.  That is exactly what they have always wanted because not one of them has any competence whatsoever in any area of science; despite their “credentials.”

    Today we have the advantage because all those decades of crap that the ID/creationists have generated is now publicly recorded, and it belongs to them.  They can no longer get away from the stench of it.  We can pull it up at any time and grind their faces in it while teaching students and the public how fraudulent science is generated.

    UD is a pile of self-indulgent, pseudo-intellectual wannabe movers and shakers of society.  Let it stand as a monument to those too lazy or incompetent to learn.  Don’t engage them; study them and learn what NOT to be.

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