What is the Plan?

A prominent ID supporter at UD, gpuccio, has this to say:

My simple point is: reasoning in terms of design, intention and plans is a true science promoter which can help give new perspective to our approach to biology. Questions simply change. The question is no more:

how did this sequence evolve by some non existent neo darwinian mechanism giving reproductive advantage?

but rather:

why was this functional information introduced at this stage? what is the plan? what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?

 

Gpuccio references actual biology in his writings and is one of the few at UD that do, and as such I’m prepared to take him at his word that the ID project is now ready to move from simply determining design to answering the questions he posed:

  • why was this functional information introduced at this stage?
  • what is the plan?
  • what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?

If any ID supporter would like to provide a specific example with answers for those 3 points for discussion that would be perfect.

Gpuccio’s OP concludes:

The transition to vertebrates was a highly engineered process. The necessary functional information was added by design.

In response I simply repeat back the question what is the plan?

 

328 Replies to “What is the Plan?”

  1. Rumraket Rumraket
    Ignored
    says:

    Mung: Here’s gpuccio on the subject:

    “On the other hand, missing intermediates, imaginary pathways, connections in proteins space, are all conjectures without a trace of support from facts, and against any rationale.”

    He denies reasoning from missing data. So either he is contradicting himself or you and your pals here at TSZ are misrepresenting him.

    This is brilliant, that’s a textbook designer of the gaps argument.

    Presumably, if in Gpuccio’s view we had the data, he would not infer design. But, in his view we don’t, so he infers design.

    There’s a gap -> design must be the solution.

    Thank you for confirming the basic fallacy Mung.

    gpuccio: Well, they may think that they are open minded, skeptics, capable of respectful discussion.

    Well, they are not.

    I think he should spend less time crying about the tone and more time addressing the subject. That’s just me I guess.

    For all proteins which exhibit a total functional information (or an informational transition) higher than an appropriate threshold (150 bits are good, for me), and…

    Yeah, here Gpuccio is simply telling of which proteins the thinks our knowledge of is a “gap”.

    We can’t show detailed evolutionary pathways for “proteins which exhibit a total functional information higher than 150 bits” – therefore design.

    Even if we ignore the false premise (we can, in fact, show that for many examples of complex proteins), it’s still patently a design-of-the-gaps argument. But rather than EVERYTHING being designed (yet he also explains that he actually thinks that), he’s just specificying that in particular, proteins that exhibit some particular quality (150 bits of functional information) and for which we lack an evolutionary account (you know, about which we have a gap in our knowledge), must have been designed.

    Again, presumably, if we didn’t lack such accounts, he would not infer design. I could be wrong of course and he could be universally applying gaps-reasoning to everyting by simply declaring that it’s all gaps.

    Then Rumraket went on to ignore everything before that and…

    I don’t participate at UD. I read what other people post here and respond to that, where it is relevant to the subject matter: Which is the density of function in protein sequence space and whether the experiments having been done shed any light on that. And when somebody commits a basic fallacy to try to deny the evidence, I point that out. I don’t have to address everything they say, such as the whole “functional information” red herring. Either function exists in sequence space such that relatively little evolution can find it in a reasonable timeframe, or it does not, and the fact of that matter is independent of what measure of information you want to use to assign a bit-value to the size of the protein in question.

    I know you ID types are thoroughly impressed by technical jargon and quasi computer-science and engineering related terminology, but I’m not. You can blather about “functional sequence complexity”, “complex specificed information” and “upper probability bounds” until you are all a deep purple color in the face, it will impress noone but yourselves.

    I am perfectly capable of “contributing substantially instead of just offering vapid commentary,” but have to ask myself why should I? Who here really wants honest respectful dialogue?

    I want honest dialogue, I don’t respect you however. You’re clearly a know-nothing idiot with a religious agenda and I will treat you as one. That means I will take on the role of teacher and I will see you as a slightly retarded, unruly child. I don’t think you’re intrinsically subnormally mentally gifted, but I think your “parents” have intellectually abused you by feeding you too much misinformation at too early an age. As a consequence I know I probably can’t reach you, so I will just put the facts out there your feelings be damned and you will either get them if you allow yourself to think critically about it, or you won’t and all will be as it has been for decades. You will remain a know-nothing idiot with a religious agenda, or you will understand a little bit more about the natural world. The outcome will be up to you, but if your concern to begin with is tone (or your oh-so-precious religious faith, rather than what real-world facts say), you might as well just shut the fuck up and not bother responding in this thread at all.
    Nobody is here because they owe you anything, yet we’re all giving you our time anyway. Time I could be spending, probably better, on fucking pornhub, or scratching my ass.

  2. Richardthughes Richardthughes
    Ignored
    says:

    Mung,

    Then you add nothing.

  3. Mung Mung
    Ignored
    says:

    Rumraket: Presumably, if in Gpuccio’s view we had the data, he would not infer design. But, in his view we don’t, so he infers design.

    There’s no reason to presume anything.

    gpuccio:

    all proteins which exhibit a total functional information (or an informational transition) higher than an appropriate threshold

    Missing data is simply not enough reason to infer design. Something actually present is required.

    The inference to design is not based on missing data. It is based on the data that is present. Now if you ever manage to come up with the missing data, the inference can be falsified.

    So not only is his argument not a “designer of the gaps” argument, it is also a claim that can be falsified.

    That has to hurt.

  4. Mung Mung
    Ignored
    says:

    Richardthughes: Then you add nothing.

    Pot. Kettle. Black.

  5. Allan Miller
    Ignored
    says:

    OMagain,

    I will just answer this brief question from Allan Miller, who remains after all one of the most “normal” people there:

    Hey! You take that back!

    Me: “Good grief! ID of organismal proteins – how non-conjectural is that? Or is gpuccio of the “ID is not a science” school?”

    GP: ID explains facts, and is motivated by facts. Functional information in proteins is a fact. My OP here is about facts.

    The information in protein is a fact, but that does not make ID the explanation for it. That is a conjecture, at least as much as that for which the ‘darwinists’ are being derided. More so, I’d say, but of course I am biased.

    I copy here my question at #215. About a fact:

    “Astrotactin 2 is a 1339 AAs protein. 889 of them are identical in sharks and humans.The positives are 1048.

    I would really appreciate if our friends at TSZ could comment about this very simple fact.”

    Without doing any research, I would say that this is due to the proteins being commonly descended.

    On the other hand, missing intermediates, imaginary pathways, connections in proteins space, are all conjectures without a trace of support from facts, and against any rationale.

    That is hardly justifiable. The rationale is clear.

    It is not a reasonable expectation that all intermediates would be preserved and discoverable forever, given evolution. The possibility of a natural phenomenon of missing intermediates needs to be given due weight, not wafted away. One is not compelled to conclude ‘design’ for every last differential between relatives. Design is simply a competing postulate, not a ‘fact’.

    Connections in protein space are routinely demonstrated by selection experiments. Harder to do in vivo, but the existence of related proteins in related organisms is supportive of there being a connection. If one wishes to suppose Design in every single amendment – that no amendments are ever done by mutation – that cannot be refuted, but it is hardly a compelling argument.

    And what would prevent a sufficiently powerful designer from generating a navigable peptide space? Why would a Designer not wish to permit adaptation?

  6. colewd
    Ignored
    says:

    Allan Miller,

    I will just answer this brief question from Allan Miller, who remains after all one of the most “normal” people there:

    Hey! You take that back!

    Your making a serious challenge to Mung for this years dry humor trophy. 🙂

  7. Mung Mung
    Ignored
    says:

    My humor is all wet! Give the trophy to Allan. I think he’s at least a Brit. I still haven’t managed to figure out how a group of people who are all wet still manage to keep their humor dry. I’ve heard they use the bones of the Scots. Is that true?

  8. CharlieM CharlieM
    Ignored
    says:

    Rumraket,

    Hi Rumraket,
    The reason a simple soul like myself can get the gist of Gpuccio’s argument and you don’t seem to be grasping it must be because I have followed the link and read his op at UD and you obviously haven’t. He is not making gap arguments but is giving us actual details of specific proteins and their relationships.

    How can you challenge his arguments, how can you know how much time he spends “crying about the tone” compared to “addressing the subject”, and why do you feel qualified to teach Mung if you yourself are not willing to learn what Gpuccio’s argument is? You cannot seriously argue against his position if you are not willing to go to UD to see for yourself what his argument is. Its blatantly obvious that in order to critique a piece of writing the critic must first read that writing.

  9. Mung Mung
    Ignored
    says:

    Rumraket: I don’t participate at UD. I read what other people post here and respond to that

  10. Rumraket Rumraket
    Ignored
    says:

    Mung: Missing data is simply not enough reason to infer design. Something actually present is required.

    Yeah, 150 bits of functional information. So that’s still gap-reasoning. No amount of waffling is going to make it go away. It doesn’t matter how many facts Gpuccio can list about the protein, when one of the criteria for him inferring design is missing data, the argument is unavoidably a gaps-argument.

    The protein in question has quality A, B, C, D, E.. and so on(one of which is 150 bits of “functional information”), and we are lacking a detailed evolutionary account, therefore – design.

    That’s a gap-argument.

    This lesson in spotting basic fallacies in elementary logic was free.

  11. Rumraket Rumraket
    Ignored
    says:

    CharlieM:
    Rumraket,

    Hi Rumraket,
    The reason a simple soul like myself can get the gist of Gpuccio’s argument and you don’t seem to be grasping it must be because I have followed the link and read his op at UD and you obviously haven’t. He is not making gap arguments but is giving us actual details of specific proteins and their relationships.

    How can you challenge his arguments, how can you know how much time he spends “crying about the tone” compared to “addressing the subject”, and why do you feel qualified to teach Mung if you yourself are not willing to learn what Gpuccio’s argument is? You cannot seriously argue against his position if you are not willing to go to UD to see for yourself what his argument is. Its blatantly obvious that in order to critique a piece of writing the critic must first read that writing.

    There are no amount of additional filler facts about the proteins in question that can alter the fallacious inference that design should be inferred because a sufficiently detailed evolutionary account is also(in addition to those filler facts), in Gpuccio’s view, missing (unless, of course, one of those facts is that the protein couldn’t possibly have evolved).

    All Gpuccio can do, that I’ve missed out on, is list a whole bunch of facts surrounding the proteins. I don’t have to read all of them to know that once he also includes missing data as one of the criteria for inferring design, the entire argument is tained by a basic fallacy. There is no way around this. You all need to get over the cold hard logic. I recommend changing the argument, instead of trying to defend a sinking ship. There may be another way to infer design, but Gpuccio’s fallacious argument isn’t it. Back to the drawing board.

  12. OMagain
    Ignored
    says:

    CharlieM: He is not making gap arguments but is giving us actual details of specific proteins and their relationships.

    Regardless of those details, once a history is determined that protein stops being ‘designed. As gpuccio himself says. So the list of facts and relationships does not matter, all that matters is their causal history. When that is known, not design, when it is not, design!

    CharlieM: The reason a simple soul like myself can get the gist of Gpuccio’s argument

    Has your simple soul noticed that gpuccio has not actually answered any of his own questions as noted in the OP?

  13. CharlieM CharlieM
    Ignored
    says:

    Allan Miller: Connections in protein space are routinely demonstrated by selection experiments. Harder to do in vivo, but the existence of related proteins in related organisms is supportive of there being a connection. If one wishes to suppose Design in every single amendment – that no amendments are ever done by mutation – that cannot be refuted, but it is hardly a compelling argument.

    Hi Allan

    And that is why Gpuccio does not make that argument.

    Do you understand the relevance of the 6275 novel bits that he gives for the six proteins? In other words their similarity (or lack of) between those of vertebrates and those of pre-vertebrates. This is far removed from a single amendment.

    We need not consider intermediates when we are comparing what existed at some specific time with what existed at some later time. The argument does not depend on the route taken from A to B but on the difference between the two points A and B.

  14. Rumraket Rumraket
    Ignored
    says:

    CharlieM: Do you understand the relevance of the 6275 novel bits that he gives for the six proteins?

    I do: The relevance is none at all. It is completely irrelevant. The synthetic measure of information he uses has zero impact on how the protein in question came about.

  15. OMagain
    Ignored
    says:

    CharlieM: This is far removed from a single amendment.

    Then gpuccio should turn to the questions given in the OP now that design has unambiguously been determined.

    why was this functional information introduced at this stage?
    what is the plan?
    what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?

    For the 6275 novel bits those questions are applicable. I await answers!

  16. CharlieM CharlieM
    Ignored
    says:

    OMagain:
    Has your simple soul noticed that gpuccio has not actually answered any of his own questions as noted in the OP?

    When scientists ask questions it is usually because they are looking for answers not because they already know the answers. Do you think that when scientists first began to ask what caused the differences in organisms such as Mendel’s peas that they already knew the answers?

  17. Allan Miller
    Ignored
    says:

    CharlieM,

    Hi Allan

    And that is why Gpuccio does not make that argument.

    No, I was doing a reductio ad absurdum. gpuccio actually sets some threshold. But if one looks at common descent (as a possible explanation for the degree of similarity), it is clear that a 1 bit change per N generations will multiply up to x changes in xN and exceed the ‘design’ threshold without a Designer ever needing to coming near it.

    Do you understand the relevance of the 6275 novel bits that he gives for the six proteins? In other words their similarity (or lack of) between those of vertebrates and those of pre-vertebrates. This is far removed from a single amendment.

    Yes. See above. We don’t have ‘pre-vertebrates’, we have their descendants.

    ?We need not consider intermediates when we are comparing what existed at some specific time with what existed at some later time.

    We must, if there is a possibility of a series of parent-child relationships. Every step change is ‘intermediate’ between the original and the current sequence.

    The argument does not depend on the route taken from A to B but on the difference between the two points A and B.

    Well, we don’t have A, if A is the ancestral sequence. We have two sequences at the branch-ends of a capital V, and A was at the base. It is clear that independent change between two lineages can accumulate, over the years, into a large gap. If Design is not invoked at the tiny steps, what compels us to invoke it for the greater, cumulative change? How do you rule out the cumulative scenario? Or is it up to me to rule it in?

  18. OMagain
    Ignored
    says:

    CharlieM: Do you think that when scientists first began to ask what caused the differences in organisms such as Mendel’s peas that they already knew the answers?

    I know that as well as asking they did work. If they ‘just asked’ nothing would have happened. As far as I can tell, gpuccio is ‘just asking’ and as such nothing will happen. And yet who else will do that work if not him? Nobody.

  19. OMagain
    Ignored
    says:

    gpuccio,

    bill:

    “The TSZ guys are bringing designer of the gaps arguments out. The use of straw-man arguments appears to signal the end of a viable challenge to your arguments at this point.”

    I agree.

    We are going back to the beginning. CLAVDIVS started with a God of the gaps argument at #44.

    After having discussed that point in detail (see especially #86) I hoped that was that, but here we are again: our friends at TSZ, having no more arguments, are back to “designer of the gaps”.

    Well, at least they must have noticed that I have never made any reference to God. I should consider that progress, but I don’t know why, I am not so sure.

    The discouraging truth is: these people are well ready to pretend to discuss as far as they think they have obvious confutations of the opponent’s position. But, when their confutations meet explicit answers, they simple avoid any recognition of those answers. Which does not mean to agree, but simply to admit that some answer has been given.

    But no, one who gives answers becomes immediately a fool, a crypto-creationist, you name it, and arguments are abandoned to leave room to name calling, or other trivialities.

    The discussion at TSZ started about my mention of a plan. I have clarified what plan I meant. I have answered the stupid objections about considering humans the purpose of the plan (which had never been part of my reasoning). I have explained why I was using human molecules, answering the objections about that.

    We have discussed the infamous desk of cards argument. We have discussed Keefe and Szostak. We have discussed natural selection and intelligent selection. And many other important points.

    We have discussed my metrics based on conservation. Any kind of objections have been made. I have answered them.

    I have even presented a paper which uses a conservation based metrics.

    Has anyone considered my points, even to refute them? No. Each time I give a reasonable explanation, they go back to other old “arguments”, and in the end to name calling.

    Well, they may think that they are open minded, skeptics, capable of respectful discussion.

    Well, they are not.

    Of course, each of them is different, and I should make some acknowledgments of partial goodwill, occasionally. Even keiths has agreed with me on one point.

    But the general trend is discouraging. With all respect, due or not.

    So there you go. Nobody has many any cogent points in response to gpuccio’s posts. Simple as that.

    We have discussed Keefe and Szostak.

    And you got it wrong and ignored correction from those more knowledgeable than you. It’s funny how you can just brush all that under the carpet – yes we discussed it and I was shown to be wrong but don’t care is how it seems to be.

  20. Allan Miller
    Ignored
    says:

    I can’t say I’ve spotted any name-calling, although ‘designer of the gaps’ is I suppose dismissively worded. It’s certainly not the only dismissive wording that has been brought to bear on the debate. It is hard to discuss alternative explanations for data when people are on such a hair-trigger to take offence.

  21. Rumraket Rumraket
    Ignored
    says:

    It’s noteworthy that colewd suddenly disappeared over to UD to have Gpuccio carry the flag for him, and we don’t get to hear any more about those supposedly harder to evolve nuclear proteins.

    And that Gpuccio’s case seems to have devolved into some silly blather about “bits of information”.

  22. CharlieM CharlieM
    Ignored
    says:

    Allan Miller: We don’t have ‘pre-vertebrates’, we have their descendants.

    Yes and it is these descendants that gpuccio uses in his/her comparison. Do you think it is legitimate for scientists to infer historic phylogenetic trees from conserved sequences?

  23. dazz dazz
    Ignored
    says:

    Rumraket: And that Gpuccio’s case seems to have devolved into some silly blather about “bits of information”.

    I’m still particularly interested in this topic. Once again, I acknowledge my limitations so any correction is appreciated.

    Gpuccio cites this paper to support his methodology to measure “functional information”

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851721/

    By comparing the evolutionary conservation of RRM residues with their ability to function in the context of the yeast Pab1 protein, we could implicate some residues in yeast-specific functions.

    this is how the authors describe the method to calculate conservation:

    Calculating RRM conservation

    To evaluate the general conservation of residues in RRMs by an unbiased approach, we searched the protein databank (PDB) for RRM domains using the terms “RRM” and “RNA Recognition Motif” and collected the PDB-ID of all proteins with a known RRM structure. Using these IDs, we extracted all of the sequences of the structurally defined RRMs from the UniProt Knowledge Base with the exception of proteins with multiple structurally resolved RRM domains, where we randomly selected a single domain for the analysis. Taking this approach provided us with 119 RRM sequences, all from unique proteins (see Supplemental Table 3 for the list of sequences). Multiple sequence alignment was performed using the MAFFT program (Katoh and Toh 2008), and a conservation score for each site was determined by the Protein Residue Conservation Prediction program using the Jensen-Shannon divergence (JSD) scoring method (Capra and Singh 2007).

    I may be inadvertently pulling one of those creationist gimmicks where a paper I don’t understand seems to support a point I’ve made, but isn’t this what one should need to do to compute conservation of those proteins in vertebrates? namely, compare ALL the available sequences, not just sharks vs lancelets and metazoans

  24. Patrick Patrick
    Ignored
    says:

    Rumraket:
    The fact that the very first pool of random sequences were immediately functional is a problem to explain for Gpuccio, if the sequence space should be mostly dead. What colossal luck the reasearchers must have had, to just so happen to start the experiment at a functional area in a largely dead sea, right? It’s funny how this is a consistent result with these kinds of experiments. It’s almost like sequence space is actually replete with function.

    You’ve identified the next line to which the intelligent design creationists will retreat. “Sequence space is replete with function! That couldn’t happen by accident! Checkmate, Darwinists!” Dembski et al. are have already started with their “search for a search” nonsense.

  25. Patrick Patrick
    Ignored
    says:

    OMagain:
    gpuccio: And no, I am not of the “ID is not a science” school. ID is science. Completely empirical science.

    I invite gpuccio to start a thread here with a post describing the scientific theory of intelligent design and its empirically measurable entailments.

  26. Allan Miller
    Ignored
    says:

    CharlieM,

    Yes and it is these descendants that gpuccio uses in his/her comparison. Do you think it is legitimate for scientists to infer historic phylogenetic trees from conserved sequences?

    As long as they are not too conserved, then sure. Phylogeny is inferred from patterns of similarity and difference. 100% one or the other, there’s no phylogenetic info.

  27. Allan Miller
    Ignored
    says:

    dazz,

    isn’t this what one should need to do to compute conservation of those proteins in vertebrates? namely, compare ALL the available sequences, not just sharks vs lancelets and metazoans

    The more the merrier, certainly! Not least to reduce stochastic noise with a small sample of 2.

  28. dazz dazz
    Ignored
    says:

    Dionisio @ UD collecting papers from his google scholar search of the terms “little is known”, “remains largely a mystery” and of course, “design”

    Lulz

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