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. gpuccio:

    Here is my complete original phrase: “At present, the number of naturally selectable intermediate for that context is easy to determine: zero. Therefore, their complexity is not knowable, and so their probability. IOWs, the only realistic model of NS is to attribute to it no role at all.”

    The added context just reinforces my point. You are saying that if we currently lack knowledge of selectable intermediates, then the only “realistic” way to model NS is to assume that there are none and that NS therefore plays no role at all.

    That’s as ridiculous as saying “I haven’t measured the air resistance of my new car design yet. Therefore the only realistic model of my car’s performance must assume that air resistance plays no role at all.”

    This is not extreme at all, and is exactly the same as my other statement: “But what I am saying is: if Joe says that he can model NS, the only model he can really build at present is to give it no role at all.”

    The phrase “the only model he can really build at present” does not mean the same thing as “the only realistic model of NS.” And as I pointed out, Joe did the right thing in his equations. Instead of foolishly assigning NS no role, as you recommend, he included fitness parameters in his equations.  His equations therefore apply both in cases where selectable intermediates exist and in cases where they don’t.  You just have to plug in appropriate values for the fitness parameters.

    You are modeling “selection” in this way. You still have no idea of which model corresponds to “natural selection”. You guys seem to miss the simple fact that “selection” and “natural selection” are not the same concept.

    Joe’s definition of fitness covers both natural and artificial selection. Your airy dismissals might be more persuasive if you actually understood what you are airily dismissing.

    Finally, you are free to think that your “nested hyerarchies” argument is evidence of selectable intermediates. That would certainly be be bad science, if it were even science, but anyone is free to think as he likes.

    Another airy dismissal sans counterargument. How do you justify the three wild assumptions you must make in order to force-fit your hypothesis to the evidence?

    1. The assumption that selectable intermediates are absent.

    2. The assumption that there is a designer who can bridge the gaps that you assume are there.

    3. The assumption that out of trillions of possibilities, the designer just happens to behave in one of the few ways that produce an objective nested hierarchy and thus make it appear that unguided evolution is operating.

    If you can’t justify those assumptions, you can’t justify ID, even in its “guided evolution” forms.

  2. A random DNA sequence can stiil be translated into a protein.

    Not only that, but ‘random’ (with caveats***) strings can completely replace the activity of a deleted, and much longer, functional protein. 

    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364 (I may have mentioned this before!)

    *** There is an element of ‘design’ – a rule is involved such that hydrophilic and hydrophobic acids are alternated in a 14-acid cycle, which is significant for folding (though by no means the only cycle that will fold). Nonetheless, the specific acid at each hydrophilic and hydrophobic site is entirely in the lap of the gods. Who see fit to provide several analogues for 4 different E. coli proteins from this otherwise totally random mishmash of acids, expressed in a library of a mere 1.5 million different sequences. Which neatly demonstrates that the ID assertion that function is ‘islanded’ universes apart is suspect, when you focus the empirical lens on the matter. Getting the basic peptide for this particular set requires a 14-acid module, hardly the biggest evolutionary task ever faced. The peptides synthesised in the study were longer iterations of that base module but still only 102 acids in length, or 306 nucleotides – and as functional as you like!

  3. GP has no way of knowing how many evolutionary steps separate a barely functional “random” sequence from an optimized sequence.

    Rather than 80 or 300 bases, we may have half a dozen. 

  4. Toronto: “That is the whole point of Dembski’s and other IDist’s improbability arguments, that something above a certain threshold needs design, not a configuration below that threshold.

    gpuccio: Completely wrong. The idea is simply that, above some appropriate threshold, some event is simply too improbable, and we refuse a random process as a credible explanation. That does not mean that the event “needs design”. Your terminology is naive, imprecise, and confounding.”

    gpuccio, the two sentences above mean exactly the same thing.

    My understanding is that English is not your first language and I believe you are rushing through the comments of many of us without completely getting an understanding of them.

    Part of my sentence can be paraphrased to mean, “Above some appropriate threshold, some event is simply too improbable, and thus a random process is not a credible explanation“.

    The part of my sentence that reads, “that something above a certain threshold needs design”, can be paraphrased to, “A bit configuration above some appropriate threshold requires a design explanation”.

    The final point, “not a configuration below that threshold ” , simply means, “a bit configuration below a design threshold does not require a design explanation”.

    gpuccio: Your terminology is naive, imprecise, and confounding.”

    The only comment I can make about that statement is that it is uncalled for.

  5. From Allan’s paper that he may have mentioned before!:

    Indeed, a collection containing just a single molecule of every one of the 20100 possible 100-residue proteins would fill a volume larger than a mole of universes. From this enormous potential for diversity, natural selection has operated over billions of years to yield a relatively small collection of sequences: Life is sustained by only ~4,000 genes in E. coli and approximately 5-fold more in humans. These considerations might lead to the supposition that genes and proteins capable of sustaining life are somehow “special.” Is this true? Or might we find functional molecular parts in a collection of artificial sequences designed “from scratch” in the laboratory?

    So, it’s not just me then!

  6. Gpuccio,

    By the way, thank you for the suggestion about setting the spell checker to english. It seems to work. I hope that will lower my rate of typos  🙂

    You’re welcome. Now if we could only get Joe G. to use the spell checker, we’d be set. I’m not sure he understands why the red squiggly line always appears under the word ‘obvioulsy’. Perhaps he thinks it’s a WordPress ‘auto-emphasis’ feature.

    Click here for amusement.

  7. gpuccio: “If I design a self-replicator below the UPB, that string has a possibility of existing due to random processes.

    No. It will probably never happen through a random process. If you really believe it can, just get it from a random process.”

    Again, you are rushing to respond without understanding the point being made.

    The threshold we choose in all our debates between every contributor on both sides, is the number of bits that we accept as being the boundary between what we accept as being possible without the mechanism of intelligent design, i.e. random processes, as opposed to those  configurations that require the efforts of an intelligent designer.

    By definition, any bit configuration under the threshold, is considered to be a possibility, in a random distribution.

    As an example it is possible to find 7 bit patterns in a random distribution that will equal ‘A’.

    Now please read the next part carefully before you respond as it may not be obvious why it is important.

    If I design a 7 bit pattern to equal ‘A’, it in no way means that all other patterns that exist with that same value, are thus no longer random.

    If random patterns can be found with the same configuration as a designed pattern, those random pre-existing patterns are still considered to be due to random processes, even though the pattern I configured with intentional design,  exists in the universe alongside them.

    The whole point of designing a bit configuration that can also be found occurring randomly, is to show the functionality of a string, that can also exist due to non-design processes.

    By designing the string, I am demonstrating it, not forcing its existence.

    Without my design efforts, the string could still exist in nature since it is below our design threshold.

    So in conclusion, I will design a string, that is also within the capabilities of non-design processes to produce.

    Since it is below the threshold, it already exists randomly and I don’t have to design it for any other purpose than to show what its capabilities are.

     

  8. gpuccio: “If you want to falsify dFSCI, you have to generate a string with dFSCI (at an appropriate threshold) entirely by non designed mechanisms. “

    Yes.

    The “dFSCI” string has to be due to non-design.

    To clarify, if I “show” you an initial string with the information to self-replicate, whose length is below the UPB threshold, are we in agreement that the string can also exist randomly without my actually creating it?

     

  9. petrushka: I continue to be amused by the fact that IDists want the respectability of mathematics, but deny the one mathematical route to modelling the process they wish to discredit.

    Mung: It just happened, that’s all, is hard to model, mathematically or otherwise.

    So you’re saying that ID models based on mathematical improbabilities, like Dembski’s CSI,  are not applicable as a tool for investigating the capabilities of biological processes?

     

  10. keiths:

    That’s as ridiculous as saying “I haven’t measured the air resistance of my new car design yet. Therefore the only realistic model of my car’s performance must assume that air resistance plays no role at all.”

    gpuccio:

    No. We know that there is air resistance, although we may have not measured it in that specific case.

    But we have no evidence that your selectable intermediates exist. They are only in your imagination, as far as we know. I am not saying that we know they don’t exist. I am definitely saying that we have no reason at all to believe that they exist.

    Would you care to apply that same standard to your Designer? Substitute ‘Designer’ for ‘selectable intermediates’, with the appropriate grammatical changes:

    But we have no evidence that your Designer exists. He exists only in your imagination, as far as we know. I am not saying that we know He doesn’t exist. I am definitely saying that we have no reason at all to believe that He exists.

    Too funny.

    And I have given you evidence that selectable intermediates exist. You didn’t deny that Lenski had found one — your only claim was that it was a case of ‘microevolution’, not ‘macroevolution’. Also, my objective nested hierarchy argument shows that the evidence supports the existence of selectable intermediates far, far better than it supports the existence of your designer.

    He [Joe F.] just invented parameters for which there is no empirical support.

    But there is support for them. Even you accept the reality of natural selection. Natural selection operates via differential fitness, so of course there are fitness parameters in the equations. How could there not be?

    You keep saying that you accept microevolution but deny macroevolution. Do you really think that microevolution never involves fitness differentials?

    keiths:

    Joe’s definition of fitness covers both natural and artificial selection. Your airy dismissals might be more persuasive if you actually understood what you are airily dismissing.

    gpuccio:

    I understand it perfectly.

    Your understanding isn’t even close to perfect if you can’t see that fitness applies to both natural and artificial selection, and both macro- and microevolution.

    I have already answered your “arguments” based on hierarchies. I won’t do it again. And they are irrelevant to the existence of selectable intermediates.

    Your answer failed to justify the assumptions you must make. Let me pose the question again:

    How do you justify the three wild assumptions you must make in order to force-fit your hypothesis to the evidence?

    1. The assumption that selectable intermediates are absent.

    2. The assumption that there is a designer who can bridge the gaps that you assume are there.

    3. The assumption that out of trillions of possibilities, the designer just happens to behave in one of the few ways that produce an objective nested hierarchy and thus make it appear that unguided evolution is operating.

    If you can’t justify those assumptions, you can’t justify ID, even in its “guided evolution” forms.

    gpuccio:

    There is only one way to prove the existence of selectable intermediates: find the. Nested hierarchies will not help.

    By your own standard, then, we must reject the Designer unless you can find him and show him directly to us.

  11. Gpuccio 722

    Be prepared for some apparently pedantic stuff below but I truly believe it is this confusion over language that hides deep problems with your dFSCI assertion. There is a point to it.

    a) No design explanation implies logically that the origin of the object is a design process. A design explanation infers a design origin. An inference is not a logical implication. It is an attempt at knowing something that we don’t really know for certain.

    Your English is better than most Englishmen – but here it has let you down. To “infer” is to draw a conclusion from … people infer things … an explanation cannot infer anything. For example, the wet umbrella implies that it is raining. I infer from the wet umbrella that it is raining. (This is a common grammatical error in English).

    The key difference as far as we are concerned is whether a design explanation logical implies a design origin or empirically implies it.

    So, what do you mean? I make a design inference for a protein, by dFSCI. Does the fact that I made that inference logically imply that the protein had a design origin? No. My inference can well be wrong, like any scientific inference.

    You may wrongly infer that a protein is designed. That is not the point.

    If you just mean that a design explanation includes the hypothesis of a design origin as part of the explanation, that is true. And absolutely trivial.

    Yes this is what I mean. And, assuming that you use includes in a reasonably normal sense (but this is getting into a real quagmire) it follows that a design explanation logically implies a design origin.

    My example of the airplane, even if analogical and not digital, shows very clearly the difference. When I give the explanation (an airplane designed the cloud image) I don’t know the origin of the cloud image, because I was not present, I have just arrived. But I make an inference, following some personal reasoning, and I give an explanation based on the hypothesis of a designing airplane. I can ask the people who were already there, and check if my inference corresponds to the facts they observed, or not.

    This the same confusion. I am not saying the pattern in the cloud logically implies that the pattern was designed or the origin. What I am saying is that if the pattern was designed that it follows logically (not empirically) that the pattern had a design origin.

     

    b) I am totally in the dark about your second request. You ask for:

    “a design origin for the configuration of a digital string where the correct explanation of the configuration of the digital string is not designed”

    What I wrote is:

    “If the origin of the configuration of a digital string was a design process (as explained before, an origin is not an object, and cannot be “designed”) then a design explanation of the configuration is empirically correct (that is, the inference made in the explanation, that the origin of the information was a design process, corresponds to facts)”.

    Therefore, if the configuration of an object has a design origin (as a fact), then certainly the only correct explanation for the emergence of that configuration is a design explanation. A non design explanation, in this case, would simply be wrong.

    So, if I understand well what you are asking for, it is simply impossible.

    Yes – but the key thing is the nature of that impossibility. I just want you to agree that if origin of the configuration of a digital string was a design process then it follows logically (not empirically) that the configuration of the digital string was designed. I think you agree with this, but these things need absolutely nailing down given the nature of the debate. If you disagree then it should be possible to describe a case where a digital string’s configuration had an origin in a design process and yet was not designed.

    What is this all leading up to? I hope that at the end of this you will agree:

    The configuration of a digital string is designed if and only if the origin was a design process.

  12. That’s exactly the point. CSI and its variants are mathematical abstractions purporting to model whether things can just happen. GAs are an appropriate exercise of CSI models. If ID proponents do not believe mathematics is an appropriate way to argue, perhaps they should avoid using Dembski’s and Behe’s mathematical models.

    But it is just silly to initiate an argument based on a mathematical abstraction and then deny that mathematics is an appropriate avenue for testing.

  13. Gpuccio 733 (edited to try and make clearer)

    I am glad you agree that:

    The configuration of a digital string is designed if and only if the origin was a design process. (X)

    And furthermore it follows from your definition of being designed. So this is logically true, not empirically true. Let’s hang on to this agreement and I will label it (X) for brevity.

    I have trouble reconciling this with:

    a design explanation implies a design origin empirically, and not logically implies it

    But maybe that is just a misunderstanding. All I am saying is that:

    A) To give a design explanation of the configuration of a digital string is to assert (among other things) that the configuration of the digital string is designed.

    Therefore

    B) To give a design explanation of the configuration of a digital string is to assert (among other things) that the configuration of the digital string has a design origin.

    (B) seems to me to be logically true as a result of your acceptance of (X) above.

    What did I miss/fail to understand?

    An additional thought added later

    You wrote:

    Yes this is what I mean. And, assuming that you use includes in a reasonably normal sense (but this is getting into a real quagmire) it follows that a design explanation logically implies a design origin.

    I don’t follow you. We have said that my explanation is probabilistic. We have said that it does not imply a design origin logically, but only empirically. My design explanation include the hypothesis of a design origin. What are you saying here? That if I make a hypothesis, that logically implies that the hypothesis is true?

    I am not saying that the hypothesis is logically true. I am saying that if the hypothesis is true then it logically implies a design origin. So, for example, it follows that if I don’t know of any plausible design explanation then I don’t know of any plausible design origin and if I don’t know of any reasonable design origin then I don’t know of any reasonable design explanation.

  14. Perhaps it would be plainer to say that evolution, as demonstrated by Lenski, is the only observed process that generates biolgical information. It is the only candidate for an explanation. Denegrating it as microevolution is equivalent to saying a falling apple is just microgravity.

  15. Gpuccio 739

    I really don’t understand this. In a design explanation, I make the hypothesis that someone designed the configuration. If, as you said, I don’t make such an hypothesis, it is because I don’t think that it is a good hypothesis. So, we could say that I don’t think that an explanation including a design origin is plausible. Is that what you mean? I think it’s the same thing you have already said.

    That will do.

    and if I don’t know of any reasonable design origin then I don’t know of any reasonable design explanation.

    I have difficulties to understand what you mean. It is always the explanation that is plausible or not plausible. Not the origin. The origin is simply true or false. An explanation that includes the hypothesis of a design origin can be plausible or non plausible. According to the true origin (design or non design) it can also be correct or wrong.

    OK. I will rephrase that slightly.

    If I cannot conceive of a design origin than it follows that I cannot conceive of design explanation.

    Is that clearer?

    Let me risk jumping ahead a bit. I will look for a couple more agreements (I am actually rather pleased with this establishing agreement bit by bit. I feel like it is avoiding a lot of misunderstandings. But it is taking a very long time and you must be getting bored).

    Agreement 1:

    Given :

    The configuration of a digital string is designed if and only if the origin was a design process.

    then it follows

    The configuration of a digital string is not designed if and only if the origin was not a design process.

    Agreement 2:

    In the case of digital strings with a function which are complex enough to exclude a probabilistic explanation then the only explanations which are known to most of society at this time are design explanations or deterministic explanations.

    I think this is logically true – but if you want to insist it is empirical it makes little difference.

  16. Toronto:To clarify, if I “show” you an initial string with the information to self-replicate, whose length is below the UPB threshold, are we in agreement that the string can also exist randomly without my actually creating it?

    gpuccio: No. If you show me that string, and if I have decided that the UPB is an appropriate threshold for the System and Time Span you are suggesting, I will simply not affirm dFSCI for it, and I will not make a design inference.

    Please, please, please, ……read more carefully.

    I can show you step by step that non-design processes can result in strings which you, gpuccio, will agree have “dFSCI”.

    However, there is nothing in my quoted statement above, that has anything to do with “dFSCI”, for the point I am trying to make for this step.

    The answer you gave has no relationship to the question I actually asked.

    “dFSCI” comes later in the process which is the whole point, that non-design processes will result in strings which you, gpuccio, will agree have “dFSCI”.

    Why are you afraid to simply answer the questions that are actually asked?

    Q1: Can random strings of any length exist without a “design mechanism” ?

    Q2: At what length are “design mechanisms” necessary?

     

     

     

     

  17. gpuccio: The existence of a designer, instead, is sorely required to explain the huge amount of dFSCI we can observe in biology.

    That is an assertion that no one on your side has even come close to providing evidence for.

    For every mountain of articles that support “non-design biology”, there is one small hill of articles that are opposed to “non-design biology”.

    There is not one single article written that supports “designed biology”.

    Any such “designer” document would need to meet the same requirements as a “non-design” treatment, in that “mechanisms” that support deign would have to be described.

    It’s one thing to say “Darwin can’t” as opposed to, “Here’s how the designer did it”.

    Show me one article that describes the methodology of the designer.

     

  18. Joe: There aren’t any articles that support non-design biology.

    That’s the type of statement that Behe used to lose Dover for the ID side and it won’t help ID’s cause in the future if ID continues to “hand-wave” away “non-design” articles.

    Show me one pro-design document that describes the designer’s actual design methodology.

    Was the “designer of life” himself alive?

  19. toronto: I can show you step by step that non-design processes can result in strings which you, gpuccio, will agree have “dFSCI”.

    Joe: Then do it already.

    That would require gpuccio to at least agree on some basic issues.

    Here’s the first.

    Issue 1: At what “bit threshold level” do we consider “non-design processes”  can operate at?

     

  20. Show me one pro-design document that describes the designer’s actual design methodology.

    It would be interesting to see any design methodology at all that does not involve cut and try. “Intelligent” selection is not different from natural selection in probability. And based on the Lenski experiment, functionality resulting from natural selection involves steps that have no obvious function that could be selected.

  21. Toronto: Issue 1: At what “bit threshold level” do we consider “non-design processes” can operate at?

    Mung: None. There are no ‘bits’ for any ‘non-design process’ to set. It follows that there is no minimal or maximal ‘bit threshold level’ above or below which a non-design process can operate.

    The whole point of coming up with a term like Dembski’s UPB is to establish the demarcation line between bit configurations of information that can only be attributed to “design processes” and those smaller less complex bit configurations that might be attributable to any “non-design” mechanisms.

    kairosfocus also uses a 500 bit threshold while other IDists have set thresholds as low as 150 bits.

    The UPB and other defined thresholds are a requirement if you intend on making an ID improbability argument.

    Please read up on this, and then come back with a threshold you consider appropriate.

     

  22. KF is fond of referring to his straw-in-a-hay-bale-a-light-year-on-its side probabilities. The authors of this paper mention that it would take a mole of universes – 6 x 10^23 spaces each billions of light years across – to hold every possible 100-acid sequence from a library of 20. And yet here we have a library of 1.6 million non-‘natural’ proteins that would together fit into about a tenth of a single E. coli cell, and we find function for not one but 4 nutritional knockouts of a possible 27 assayed. That’s some strike rate. 

    OK, they weighted the game in favour of a 4-helix fold. The patterning algorithm used yields a potential 5 x 10^52 sequences all told, so the algorithm obviously cuts down the space dramatically. I reckon the space for 5 x 10^52 would be a sphere of about 2.6 AU in radius – a mere 40 light seconds across, but still quite a haystack in which to hide this tenth-of-an-E coli needle. Suggesting that it’s not a needle at all. Or rather, the haystack is in no small part made of needles.

    What would be impressive is if GP applied his algorithm and picked out the functional sequences. He would probably (rightly) infer design in every single case, functional or not. But we knew that. What we didn’t know, without trying, is which of these part-designed proteins would function. Nor do we know, for any functional peptide, how far away is its nearest functional neighbour. But I would not bet on any great distance, given the way these flashgun pops illuminate the space. 

  23. Toronto: Show me one article that describes the methodology of the designer.

    Mung: Which designer?

    The designer that Dembski and Behe insist is a requirement for the diversity and existence of life itself.

    It’s in ID 101! 🙂

     

  24. Mung It just happened, that’s all, is hard to model, mathematically or otherwise.

    History is hard to model, if you’re looking to explain a particular result. However it happened. Plot the positions and energies of every atom in the earth-atmosphere system a week last Tuesday and see if it comes up with today’s weather on any run. Or set up a virtual casino and see whether the run of numbers duplicates a real one. Therefore God?

    ID enthusiasts seem to think that evolutionary theory should be able to ‘explain a giraffe’, in every detail, otherwise it, and any tool used in it, is wrong.

    You can look at general behaviours and the interplay of forces in such stochastic models. And one of the most striking features of them is their tendency to produce ‘design-like’ results from essentially random (but biased) processing. Because a method of discard of poorer solutions and retention of better is almost indistinguishable from an intentional process of design. It simply doesn’t need the intent bit. Cold weather will weed out those genes whose phenotypes are less robust in cold weather; a prolonged period of cold will see the entire population stripped of those genes in favour of the more robust. The cold couldn’t care less.

    A single round of selective fixation adds an increment of ‘designedness’ to the population; repeat rounds add further increments. This is a vital consideration for people who wish to declare that actual design is behind this or that string. If it came from a genetic process with bias, it comes from a known source of false positives.

  25. Toronto:  Q1: Can random strings of any length exist without a “design mechanism” ?

    gpuccio: Design is not a “mechanism”. However, random strings of any length can certainly exist. I have no intention to deny them this privilege.

    Again, we are having language difficulties and these difficulties are yours, not ours.

    The term “design mechanism” does not mean design is a mechanism.

    If you point out a “red Ferrari” to me I would not correct you with the statement, “Red is not a Ferrari”.

    I’d like to attempt to invalidate your “dFSCI” but I can’t if you don’t put it into a form that is falsifiable.

    If you cannot come up with a falsifiable version of “dFSCI”, it is useless as a scientific tool.

    If I can show a computer simulation of the growth of complex information without the guidance of a designer, would that invalidate “dFSCI”?

     

     

  26. gpuccio: Ah, but you are really obstinate!

    Non design processes can operate at any level. With different probabilities to give different results. All we can do is to compute the probability of a certain random outcome in a certain system. Thresholds are only artificially used for specific inferences in specific theories. (Ah, no, I must not speak of dFSCI. Yet.)

    Ah, but you are really vague!

    I want to invalidate “dFSCI”.

    Can you come up with a falsifiable description for “dFSCI”?

    This implies that there is enough information in your description to come up with an experiment that would invalidate “dFSCI”.

     

     

  27. gpuccio: a) The information in the computer is completely blind to what will be generated.

    c) The computer does not select anything.

    d) The computer does not remunerate any result.

    e) New, original dFSCI emerges.

    a) – yes.

    b) – where is it?

    c)  – yes

    d) – I don’t understand what you mean by remunerate

    e) – yes

    gpuccio: The design inference by dFSCI is fully falsifiable, as explained many times. Any string exhibiting dFSCI that emerges in a non design system can falsify it.

    Then let’s agree on a test. I don’t want to do something on my own and have you say the experiment was not valid.

    Do you agree on f) ?

    f) The software in charge of the simulation is not a part of the simulation.

     

  28. gpuccio: Design is not a “mechanism”. However, random strings of any length can certainly exist. I have no intention to deny them this privilege.

    toronto: The term “design mechanism” does not mean design is a mechanism.

    Joe: True. Design is a mechanism BY DEFINITION.

    I’m confused Joe as to who you are in agreement with.

     

  29. Gpuccio 746

    Almost there but there is a significant hurdle …

    We conceive explanations, not origins. Origins are facts, we either observe them or not.

    I cannot understand how you can say we cannot conceive of origins. As long as you can picture something in your mind you can conceive of it. And you can certainly picture origins. You can conceive someone designing something or a natural process creating a crystal which becomes the origin of something. I think you must be using some rather specialised meaning of the word “conceive”.

    I want to ask you if you agree to this:

    If I cannot conceive of a non-design explanation then I cannot conceive of non-design origin.

    But clearly we need to be sure what we mean by “conceive” before answering this.

  30. Joe 755

    True. Design is a mechanism BY DEFINITION.

    Why is it that evos have the most difficult time with using dictionaries?

    I am couldn’t resist this.  I looked up design in the online dictionary. It can be a verb or a noun. “mechanism” is a noun. So if a design is a mechanism it must be the noun meaning of “design”. Here they are listed:

    1.

    a. A drawing or sketch.
    b. A graphic representation, especially a detailed plan for construction or manufacture.
    2. The purposeful or inventive arrangement of parts or details: the aerodynamic design of an automobile; furniture of simple but elegant design.
    3. The art or practice of designing or making designs.
    4. Something designed, especially a decorative or an artistic work.
    5. An ornamental pattern. See Synonyms at figure.
    6. A basic scheme or pattern that affects and controls function or development: the overall design of an epic poem.
    7. A plan; a project. See Synonyms at plan.
    8.

    a. A reasoned purpose; an intent: It was her design to set up practice on her own as soon as she was qualified.
    b. Deliberate intention: He became a photographer more by accident than by design.
    9. A secretive plot or scheme. Often used in the plural: He has designs on my job.

    I don’t see the word “mechanism” there.  I wonder which meaning you think implies mechanism?

  31. Gpuccio,

    Evolutionary biologists (and I) claim that selectable intermediates exist and that unguided evolution is responsible for the diversity of life. You claim that selectable intermediates don’t exist, or that they are so sparse as to be unbridgeable via a Darwinian process. Therefore you claim that an intelligence must have been responsible for bridging the gaps.

    What would we expect to see if the evolutionists and I are correct? Well, unguided evolution operates via small genetic changes and primarily vertical inheritance, so we would expect it to produce a nested hierarchy. And not just any nested hierarchy, but an objective nested hierarchy, meaning that disparate lines of evidence — morphological and genetic, for example — will converge on the same tree, or very nearly so.

    That is exactly what we find. As Theobald explains, if you infer a nested hierarchy for the 30 major taxa of his Figure 1, first using morphological data and then using genetic data, you get exactly the same tree to an accuracy of 38 decimal places. Out of trillions of alternative possibilities, unguided evolution via selectable intermediates gets it exactly right.

    On the other hand, what would we expect to find if your designer hypothesis were correct? Well, you are hypothesizing an unknown designer with unspecified abilities working under unknown constraints with unknown goals. Therefore, your hypothesis makes no predictions at all. Any state of affairs would be compatible with the existence of your Designer — you could just shrug and say “I guess that’s how the Designer did it.”

    The world looks exactly — to 38 decimal places — like we expect it to look if unguided evolution is operating via selectable intermediates. Against this stunning success, intelligent design can offer nothing. It makes no prediction at all. The evidence blows it away. It’s not even competitive as a theory.

    Your argument is a futile attempt to bring ID back into the race by tacking extraneous, ad hoc assumptions onto it. But as I’ve explained, you can’t just tack on arbitrary assumptions — you’ve got to justify them.

    You’ve invented a fictional barrier to evolution by assuming that selectable intermediates do not exist. Yet you’ve been shown that the evidence is literally trillions of times stronger for the existence of selectable intermediates than it is for their absence.

    You try to rationalize this by claiming, suddenly and very conveniently, that indirect evidence, no matter how overwhelming, is no longer sufficient to establish the existence of selectable intermediates. Never mind that all of ID is based on indirect evidence. ID depends on indirect evidence, so claiming that it is insufficient when applied to evolution is a transparent double standard.

    Having assumed (without justification) that there are no selectable intermediates,  you now need a designer to get across the barren gaps. You assume the existence of a Designer who conveniently has the abilities needed to do the job.

    In other words, you invent a Designer to surmount the invented obstacle. 

    As if that weren’t ridiculous enough, you need yet another assumption to make this rickety “theory” match the evidence: you have to assume that the Designer, for whatever reason, just happens to behave in a way that mimics unguided evolution and produces an objective nested hierarchy — despite the trillions of other possibilities.

    I don’t see how you can suggest it with a straight face, especially given that the alternate hypothesis fits the evidence without the need for any ridiculous, ad hoc assumptions.

    Tomorrow I’ll address some of the specific claims you make in your latest comment to me. For now, suffice it to say that you don’t succeed in justifying the ridiculous assumptions outlined above.

  32. When arguing with IDists I think you need to be careful with the word selectable. Neutral or nearly neutral mutations pass through the sieve of purifying selection, but are not “selected for.”

    As Lenski demonstrated, neutral mutations can provide the critical scaffolding for later adaptive changes. This is what makes possible molecular inventions that span Behe’s Edge.

  33. Toronto:I’m confused Joe as to who you are in agreement with.

    gpuccio: I don’t understand why you seem to assume that we in ID should agree on everything. ID is not a dogma, it is a place for thinking persons. But we certainly agree on most things.

    The problem here is one of communication not simply taking a somewhat different position than someone on your own side.

    Two doctors debating a diagnosis would not be possible if their usage of terms was very different.

    It’s one thing to disagree on a point, but having a mismatch in definitions means someone is going to receive a message that is different then the one that was sent.

    Everyone should agree on terminology.

     

  34. Mung #730 says:

    Ok, Joe, I’ll bite. What is a GA.

    I’ll say what a GA is not. A GA is not a model of evolution.

    Sorry for the delay in answering — I have been busy. (I will shortly also reply to gpuccio’s most recent response to me.)

    A little online searching will disclose that there are various definitions, but that generally a GA is an algorithm with a representation of a finite-size population of genomes that reproduce and have multiple sites that mutate, recombine, and undergo natural selection. The fitnesses of the genotypes are chosen so that they are largest when some desired optimization problem is solved.

    In other words, a GA is a standard multilocus Wright-Fisher model (or else Moran model) of evolution, except for the particular choice of fitness function.

    Mung has some very strict distinction that Mung makes between a GA and a “model of evolution”. I have no idea what it might be, or why it is important. Don’t ask me — I’ve only been modeling evolution for 50 years now, but apparently this is not enough experience to understand what Mung is talking about.

    The effect of declaring that a GA is not a model of evolution is to rule out using it to see whether there is a general rule that CSI cannot be put into the genome by the ordinary population-genetic processes of evolution. Ruling that GAs are off-limits for this purpose is arbitrary and unjustified. 

  35. It speaks to Gpuccio’s understanding of what science is when he does not see a problem with multiple self-contradictory definitions of, in this case, dFSCI. 

    It should rather be called Gpuccio-dFSCI and Joe-dFSCI to show what particular version is referenced.

    Nobody expects everybody in ID to agree on everything but if you can’t even agree on the basics then that shows there are as many different versions of ID as there are ID supporters. 

    And the fact that they never thrash out their internal disagreements and present a unified definition they can all agree on again shows their lack of understanding of how to progress in science. Unless all can agree on the terms in use then everybody is talking about different things. 

     

  36. gpuccio: But the parameters of everything must be realistic for the situation we are modeling. So, for example, the number of states the software generates must be appropriate for the situation we are modeling.

    I don’t understand what you mean by “number of states the software generates”.

    Do you mean per “individual” or for one generation of a “population”.

    gpuccio: If we are modeling a transition from an unrelated state, the new dFSCI generated must really come from an unrelated state, with no information at all about the final target.

    There is no final target but I don’t understand “transition from an unrelated state”.

    There must be no special choice of the variables at the start of the simulation that may be related to what we expect to obtain.

    The start of the simulation must start with something within the constraints of the “environment” the software resides in.

    For instance if we were modeling biology on Earth, there is no point in attempting to model a biological configuration that only works at -200 F.

    For the same reason, a computer simulation should not bother attempting to run code that has no chance of working in its “environment”.

    Secondly, a computer simulation has the added problem that certain “code” may crash the “virtual world” while biology has no such equivalent.

    The world is not instantly destroyed by the birth of any single biological organism, but in a computer simulation, that is something that needs to be addressed.

    g) I will use a random bit generator to come up with my replicator.

    h) I will not run the code before I verify the “world will not end”.

     

     

     

  37. Gpuccio 759

    Let’s imagine (or conceive ) that we can, in our lab, put a few ingredients together, on certain strange environmental circumstances, and observe that in a certain time an object exhibiting dFSCI is generated. The result seems to be repeatable, and so we imagine that it could be explained by a necessity mechanism. But we have no idea of what the mechanism is, because it fits not with any of our understanding of physical laws. At the same time, we are controlling the setting, and we have really no reason to think that an intelligent intervention is possible. (I will ignore the possibility that a non physical designer is specially trying to confound us).

    OK this very helpful and I think draws us close to the sense in which I find your argument is circular.

    First some comments about this scenario.

    • It would be very hard to be sure that the ingredients were the origin given no mechanism – correlation is not causation. Repeated correlation under a wide range of conditions would be evidence but that is equivalent to discovering a new law of nature and a deterministic explanation! What were Newton’s laws of motions but repeated correlation under a wide range of conditions. At the time there was no mechanism.
    • If you don’t know the mechanism you have no reason to ignore the intervention of a non-physical designer who is deliberately correlating the ingredients with the configuration – not necessarily maliciously – it could be for a thousand reasons – perhaps the designer wishes to make its presence known to the experimenter by performing miraculous correlations.

    Now recall the statement in 651 which we agreed was an accurate statement of the dFSCI case.

    “In the case of digital strings with a function, if the information linked to the function is complex enough to exclude empirically a probabilistic explanation, and if there is no known deterministic explanation why the string should happen to have a configuration that performs that function, then you can infer design”. (A)

    How (A) be falsified?

    First consider the statement :

    In the case of digital strings with a function, if the information linked to the function is complex enough to exclude empirically a probabilistic explanation then the string is designed

    (this is (A) without the clause “no known deterministic explanation”)

    If we come across a functional, digital string which is too complex to have a probabilistic explanation there are four options:

    a) There is a known mechanism and the origin is designed. This is quite common.

    b) There is a known mechanism and the origin is not designed. This is also quite common. The London temperate record would be an example.

    c) There is a no known mechanism and the origin is designed. This is very uncommon, in fact it is pretty much the definition of magic or a miracle.

    d) There is a known mechanism and the origin is not designed. The type of scenario you describe. This is also very uncommon and a major scientific mystery.

    All four options: a,b,c, d would be relevant evidence. a and c would support it. b and d would be evidence against it. However, c and d are bizarre and extraordinarily uncommon because our current state of knowledge is such that we can almost always identify a mechanism to link an origin to an outcome and, as discussed above, it would be hard to be sure that origin is an origin and hard to tell c from d. They can effectively be ignored as sources of evidence. This leaves a and b.

    But if you now add back the no known deterministic explanation clause to get back to statement (A) then you have said you will not consider cases of b. So you left only with a as a realistic source of evidence for (A)

  38. Joe 761

    LoL!

    mechansim:

    b: a process, technique, or system for achieving a result

    design:

    1: to create, fashion, execute, or construct according to plan :

    So a mechanism is a process or technique for getting something done and design is to to create, fashion, execute, or construct according to plan and a plan is a method for achieving an end

    Was that too complicated for you Mark? Really?

    Joe as you are so charming and always ready to listen to the other point of view I am going to give you a free English lesson. The words of the English language are divided into parts of speech such as verb, noun, adjective, preposition, adverb, and conjunction. These parts of speech are mutually exclusive . An A cannot be a B if A and B are different parts of speech.

    Now in the example you give the word design is a verb (the word “to” at the beginning of the definition is a handy tip). The word mechanism is a noun. So in your example design cannot be a mechanism. It may be an activity done according to a mechanism – but this is not what you asserted back in 755.

  39. Joe: OK mechanisms are a way of doing things. We can do things by design or we can do things willy-nilly. Both are mechanisms in this sense- the sense that the word is being used in this debate.

    You already have evidence that gpuccio, myself and others in this debate, do not use “design” to mean mechanism in the sense that you do.

    In this debate we have two groups of mechanisms, design and non-design.

    e.g. design.mechanism_001, design.mechanism_002, etc.

    For our side to claim “non-design” as a mechanism would leave you no “specific processes” you can investigate and falsify.

    The same applies to your side in that we need “specific processes” of design that we can investigate and falsify.

    Your side has provided no “specific process” supporting the design position.

    This whole debate has centered on processes described by our side.

    Where are yours?

  40. Putting GAs off limits is neither arbitrary nor unjustified. If GAs are admitted as models of evolution, the ID hypothesis becomes superfluous.

  41. toronto: Your side has provided no “specific process” supporting the design position.

     

    Joe: Liar! Big FAT liar!

    Dr Spetner gave us “built-in responses to environmental cues”.

    But Joe, responding to the environment is an “evolutionary mechanism”, i.e. it’s ours!

    What you have described as design processes are really more equivalent to what a mechanic does in a garage.

    I want to know the processes used by the designer of life, not a human being discovering what the designer has done and altering the design.

    An automotive engineer solves questions that apply to design issues, not to service technician issues.

    How did the designer design?

    How do you design biology for an unknown future without trial and error?

    If the designer uses trial and error, how is that different from non-design trial and error?

    Give me processes Joe.

    What is the process used for foreseeing the future environment in order to even install responses to environmental cues?

  42. petrushka: Putting GAs off limits is neither arbitrary nor unjustified. If GAs are admitted as models of evolution, the ID hypothesis becomes superfluous.

    Joe: GAs model Intelligent Design evolution.

    I think you and Mung should clarify what you actually mean by a GA.

    We again have different meanings for the same term.

    Why don’t you and Mung flowchart a GA so we can have some understanding of what you mean by the term.

     

  43. Joe 768

    It is so kind of you to spend time preparing these amusing faux pas of logic and misuse of dictionaries – much appreciated. I think I have spotted all the mistakes – but do tell me if I have missed any.

    Originally you wrote:

    Design is a mechanism BY DEFINITION.

    Then to back this up you wrote:

    mechansim:

    b: a process, technique, or system for achieving a result

    design:

    1: to create, fashion, execute, or construct according to plan :

    So a mechanism is a process or technique for getting something done and design is to to create, fashion, execute, or construct according to plan and a plan is a method for achieving an end

    Equating a verb with a noun. (I got that one last time).

    When challenged you switched to a different definition of design (that was easy to spot):

    b: a plan or protocol for carrying out or accomplishing something (as a scientific experiment); also: the process of preparing this

    This turns out to be one of ten definitions of design as a noun (a bit of research required – but the letter b at the beginning was a clue).

    Also turns plan has four definitions as a noun – one of which is method for achieving an end (a bit harder – no clue provided).

    So:

    • Design can mean ten different things – one of which is plan or protocol.
    • Plan can mean four different things – one of which might arguable be called a mechanism.

    So a design can be many things other than a mechanism. Therefore it is false that

    Design is a mechanism BY DEFINITION

    I think I got all the errors. But I didn’t understand the point of all the insults. Were they another game?

  44. There are lots of different GAs modelling different aspects of evolution. What they all have in common is the ability to test hypotheses regarding the probability of functional change.

    The problem they pose for ID is that they directly test the probability estimates of Dembski and Behe.

    Hence the necessity of ruling them out by definition.

    I simply find it amusing that ID advocates base their entire argument on abstracting chemistry to “information,” then estimating the probability of information being created by an evolutionary process, but ruling out any mathematical test of the probabilities.

    Although mathematical models of complex phenomena are always incomplete, it is interesting that Dembski and Behe think their own models of probability are infallible.

    My own thought is that if Joe or gpuccio or Dembski or Behe think that existing GAs are deficient, they should build their own and argue that their models capture something currently being missed.

    Of course Behe once did something along those lines and was quizzed on it at Dover. His own model failed to support his claim of Edginess.

  45. Gpuccio,

    As I said, you are entitled to your own opinions. I don’t agree.

    It’s a given that we are entitled to our opinions. The question is whether each of us can justify his opinions.

    The only “assumption” necessary to explain that kind of nesting in the design explanation is that the designer needs to act through common descent, and to reuse what already exists with intelligent modifications.

    No, because guided evolution via common descent doesn’t guarantee the existence of an objective nested hierarchy. You have to make additional assumptions which amount to stipulating that the designer acts in a way that is indistinguishable from unguided evolution. How do you justify the assumption that the designer is an evolution mimic?

    On the other hand, design explains the dFSCI observed in biological beings, and neo darwinism does not explain it.

    You create a gap by assuming, against the evidence, the absence of selectable intermediates. Having created the gap, you now need a Designer to fill it, so you invent one. The gap is your only reason for invoking a Designer, and it is an invented gap.

  46. petrushka: Although mathematical models of complex phenomena are always incomplete, it is interesting that Dembski and Behe think their own models of probability are infallible.

    That’s the problem with ID, that their models don’t accurately take into account physics, unless it makes something more improbable instead of less!

     

     

  47. Joe: How did the designer design?

    How did the designers of Stonehenge design Stonehenge?

    The designers of Stonehenge did not use the same processes as Lockheed engineers used to design the F-35.

    The Lockheed designers could probably design Stonehenge, but being able to move stones doesn’t mean you have the capabilities and tools required to design a supersonic fighter.

    The designer of life had a bigger challenge than either of them.

    The first challenge of the designer of life was, “What will my design face in future environments when I can’t predict what that environment will look like?”

  48. Petrushka: [neutral mutation] is what makes possible molecular inventions that span Behe’s Edge.

    Well, this and recombination. Recombination has the feature that both parts have separately been through the ‘purifying’ sieve already. They’ve never been through it in harness, of course, but two individually benign elements are more likely to reach a successful combination than a pairing where one or both, or their immediate neighbourhood, is detrimental. A sequence that cannot be reached from either by point mutation due to surrounding detriment can be reached by combination.  Point mutation is probing at the same time, of course. Every change is.

    Behe’s ‘Edge’ is based on two serial mutations, but there is a significant probability of the two mutations existing separately in the population and recombining which needs to be added in. Related to the ‘birthday paradox’, it takes surprisingly few instances to generate a significant probability of occurring.

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