Promiscuous Domains and Motifs Are Better Explained by Common Design than Common Descent, (Sal’s module Hypothesis)

Dr. Winston Ewert put forward his module hypothesis, but I put forward an alternate module hypothesis at the domain and motif level of proteins. It is based actually on papers by evolutionists who have pointed out that the problem of “Promiscuous Domains” remains an unsolved problem in evolutionary biology.

When I put Promiscuous Domains on the table in the Common Design vs. Common Descent thread, the TSZ Darwinists ignored the problem and then declared victory. I viewed their non-response as evidence they didn’t understand the problem and/or preferred to ignore it.

Perhaps pictures are worth ten thousand words. From the NIH, that great source inspiration for the Intelligent Design community, we have the CDART database viewer.

From the CDART viewer, I provide a few of the thousands of diagrams that show the promiscuity of protein domains. The diagrams below show the classical zinc finger ZF-C2H2 “ZF” domain and the Plextrin Homology “PH” domains. Note how the location of domains is “shuffled” to different locations in different proteins. It’s as if proteins are made by different lego-like parts in different order and position. My preliminary look into small 4-amino acid motifs that are the target of phosphorylating kinases suggests the the problem of promiscuity goes all the way down to small motif levels.

Such promiscuity is more consistent with common design than common descent.

Click to Enlarge Classical ZF-C2H2 Zinc Finger Page 5
zf 5

Click to Enlarge Classical ZF-C2H2 Zinc Finger Page 157
cf 157

Click to see all CDART Classical ZF-C2H2 Zinc Finger Architectures

Plextrin Homology Page 1
ph 1

Click to Enlarge Plextrin Homology Page 5
ph 5

Click to see all CDART Plextrin Homology Architectures

1,004 thoughts on “Promiscuous Domains and Motifs Are Better Explained by Common Design than Common Descent, (Sal’s module Hypothesis)

  1. petrushka: You can’t really know that an atom exists unless it interacts with another particle.

    exactly my point

    peace

    OMagain: If FMM’s ideas had value they would be spreading of their own accord.

    How do you think I heard about them?

    peace

  2. Zachriel: “I like apples” is a statement concerning the state of mind of the utterer, and the person can change their mind at any time.

    fifthmonarchyman: That is your subjective opinion. I would disagree

    You disagree that “I like apples” is a statement concerning the state of mind of the utterer? Seriously? Or that a person might change their mind about liking apples? Really?

    fifthmonarchyman: Each of the observers are only reporting what they subjectively think are toes.

    In the case of counting toes, multiple independent observers can verify the number of toes, while “The apple was delicious” is only found in the mind of the utterer.

    Regardless, we have shown what we sought to show about your view. It is based on a fundamental precept that the vast majority of readers will rightly reject, that there is no epistemological difference between someone saying “The apple was delicious” and “There are five toes on that foot.”

    ETA: Eppur si muove

  3. stcordova: No it’s not mentioned. How do you suppose it got there and persisted. You can invoke exon shuffling if you want, but how reasonable is it that one will get coherent function just by shuffling exons? Where is the demosntration from first principles this is an ordinary expectation of from random variation and common descent?

    Now I am confused. Is convergence your word for the re-use of modules or did you mean convergent evolution of all the individual protein domains from unrelated sequences (which would be an enormous strawman).

    I would certainly invoke recombination and transposition events. They are well described and explain the observed patterns perfectly fine. If you want to dispute that, you need to put some meat on that claim. For example, you could demonstrate that the exact architecture of these proteins is invariant among species as they are intolerant of all mutations without losing coherent function (Spoiler: no they are not).

    stcordova: When is a theory not much more than just mere assertions of “it just happened that way” vs. a mechanistic description of why this is consistent with ordinary expectation of ordinary processes? Evolutionary theory is not much more than saying, “it happened by ordinary mechanisms because it just happened, JUST SO” That’s not a mechanistic theory.

    That’s funny, I was going to say something similar about Common Design.

  4. Zachriel: Or that a person might change their mind about liking apples? Really?

    I disagree that a person can change his mind at any time.

    I think that one changes his mind only when circumstances change.

    I don’t think I could simply decide to quit liking apples.

    Zachriel: In the case of counting toes, multiple independent observers can verify the number of toes, while “The apple was delicious” is only found in the mind of the utterer.

    That “Zac likes apples” can be verified by multiple independent observers.

    The conclusion that there is an apple in my hand is reached in the minds of the folks who conclude thusly.

    Zachriel: It is based on a fundamental precept that the vast majority of readers will rightly reject

    yes yours is the majority viewpoint at a website frequented by atheists who in the main hold to empiricism.

    That tells you very little about the idea’s validity. It tells you nothing about why anyone who does not hold to that school of thought should find the statement “special creation would not result in the objective nested hierarchy we see” to be a compelling argument.

    peace

  5. fifthmonarchyman: I don’t think I could simply decide to quit liking apples.

    People’s tastes do change.

    fifthmonarchyman: The conclusion that there is an apple in my hand is reached in the minds of the folks who conclude thusly.

    Sure, they hold the thought in their minds, but it is independently verifiable, unlike “The apple was delicious.”

    fifthmonarchyman: That tells you very little about the idea’s validity.

    It does for those who reject your solipsism. Sure, everyone could be a p-zombie. Sure, the universe could just be a movie playing in your mind. And while such ideas are food for thought, they are scientifically vacuous.

    In any case, we can define science methodologically. Assume the universe exists. Assume other observers exist. Define subjectivity as the individual perception, and define objectivity as the ideal from a defined process of minimizing subjectivity through independent verification. Define the scientific method as a specific iterative means of testing hypotheses.

    Now, you can believe whatever you want. You can adhere to your solipsism, handwaving to your heart’s content. You don’t have to believe the system converges on answers, or that it matters in the least. You can be Zen, and believe that there are no distinct entities, that the universe is One — as long as you act as if entities exist.

  6. Zachriel: You can adhere to your solipsism, handwaving to your heart’s content. You don’t have to believe the system converges on answers, or that it matters in the least. You can be Zen, and believe that there are no distinct entities, that the universe is one — as long as you act as if entities exist.

    Actually ,I believe fifth’s point is without the justification of omniscience and the power of revelation to impart objective knowledge to humans, all man’s efforts can be reduced solipsism.

  7. newton: How was it designed might be helpful in evaluating its reasonableness. Any ideas?

    I’d start by asking them to solve the cart-before-the-horse problem with “design.” ID supposedly takes clues to design from human design, but they forget a tiny little detail: they’re trying to explain things that make our capacity to design possible.

    For example, regulatory interactions are required for our brain development, for the expression of genes related to brain function, for the very workings of our brain activities. Since design requires such things, design cannot be their source.

    This is where ID breaks down into revealing its true nature: mere religious fanaticism/fantasy.

  8. The problem I’m encountering right now is identifying the intron exon boundaries of ZNFP genes. Some genes are nicely annotated and recorded and the introns and exons are automatically shown and highlighted in the gene in the chromosomes. Not so, apparently for the ZNFP genes I’m looking at so far. Ugh!

  9. newton: Actually ,I believe fifth’spoint is without the justification of omniscience and the power of revelation to impart objective knowledge to humans, all man’s efforts can be reduced solipsism.

    All human experience can be reduced to solipsism, with or without revelation, revelation being just another experience of a “brain in a vat“. All systems of knowledge have to have some assumptions to form a logical foundation. Fifthmonarchyman rejects certain of these assumptions in lieu of others that put his personal revelation in a privileged position.

  10. stcordova:
    The problem I’m encountering right now is identifying the intron exon boundaries of ZNFP genes.Some genes are nicely annotated and recorded and the introns and exons are automatically shown and highlighted in the gene in the chromosomes.Not so, apparently for the ZNFP genes I’m looking at so far.Ugh!

    Remember Sal: Recombination doesn’t need to happen at exon boundaries. I suspect that for many zinc fingers, the original recombination events, even if they did happen at exon boundaries, happened long ago enough that the original boundaries might have been lost since.

  11. Zachriel: All human experience can be reduced to solipsism, with or without revelation, revelation being just another experience of a “brain in a vat“. All systems of knowledge have to have some assumptions to form a logical foundation. Fifthmonarchyman rejects certain of these assumptions in lieu of others that put his personal revelation in a privileged position.

    That would be correct, however because one of his assumptions is it is logically possible that Divine Omnipotence can render an assumption into an objective fact and be known by revelation ,his foundation no longer rests on an assumption but by revealed truth, maybe. But maybe is better than any alternative.

  12. Zachriel: Regardless, the ‘liking’ can’t be observed.

    I think the time may come when we can observe the liking. We have good operational definitions of liking. They involve observing preferences. It is not out of the question that we may develop ways of observing brain behavior.

  13. newton: Actually your point is everything is equally subjective.

    Not my point at all.

    My point is that everything that originates from finite biased human beings is equally subjective.

    That does not make all our opinions worthless or equally warranted. It only means that they are all subjective.

    Peace

  14. Zachriel: People’s tastes do change.

    Yes and apples decompose to the point that they are no longer apples.

    It’s also important to keep in mind that peoples tastes don’t change for no or random reasons. And they can’t decide to change their tastes “at any time”

    Zachriel: It does for those who reject your solipsism.

    I’m not a sophist. Far from it. I think that sophism or absurdity is the necessary result of any worldview that consistently rejects God.

    Zachriel: All human experience can be reduced to solipsism, with or without revelation,

    I’d love to see you support that claim, care to start an OP?

    Zachriel: All systems of knowledge have to have some assumptions to form a logical foundation.

    I agree. The existence of God is unique in that it is both an assumption and inescapable revelation.

    Question assumptions other than the existence of God and you end up with sophism or absurdity.

    Question the assumption that God’s existence is necessary for knowledge and you end up with renewed confidence that God does exist.

    Zachriel: Fifthmonarchyman rejects certain of these assumptions in lieu of others that put his personal revelation in a privileged position.

    No, I endeavor to reject assumptions that inevitably lead to sophism or absurdity and accept those that are left.

    I recommend that process to anyone who wants to be a consistent thinker

    peace

  15. fifthmonarchyman:That does not make all our opinions worthless or equally warranted. It only means that they are all {equally} subjective.

    You insist upon using the terms subjective and objective as a neat dichotomy, even though the terms are often used as a continuum, with objective being an ideal that is approximated by a process of independent verification. You want to call it a continuum of warrant, as if the word is what matters.

    petrushka: It is not out of the question that we may develop ways of observing brain behavior.

    You are conflating the property of the person with a property of the apple. “The apple is delicious” is subjective, and will vary with the taster. “This is an apple” is objective, because it can be independently verified.

  16. Entropy: I’d start by asking them to solve the cart-before-the-horse problem with “design.” ID supposedly takes clues to design from human design

    You won’t be surprised to know that I think you have it exactly backward.

    The reason we recognize human artifacts as “designed” is because we recognize similarities with archetypal design in creation.

    Entropy: but they forget a tiny little detail: they’re trying to explain things that make our capacity to design possible.

    We can design because we are created in the image of our creator.

    As such you would expect to find similarities between our behavior and his.

    peace

  17. Zachriel: You insist upon using the terms subjective and objective as a neat dichotomy, even though the terms are often used as a continuum

    Not by anyone who is not butchering language and flouting logic.

    You might as well claim that “circle” and “square” exist in a continuum and therefor a circular square is possible.

    I would not expect you to understand things like the law of noncontrdiction give your insistence to refer to yourself in the plural.

    Zachriel: “The apple is delicious” is subjective, and will vary with the taster. “This is an apple” is objective, because it can be independently verified.

    You are ……still not getting it

    I think “The apple is delicious”
    and
    I think “This is an apple”

    Are equally subjective.

    That goes for the same sentences when the “I think” is silently implied

    Zachriel: “This is an apple” is objective, because it can be independently verified.

    No it can’t.

    All you can independently verify is that conditions consistent with the hypothesis that “this is an apple” seem to exist.

    You can do exactly the same with any hypothesis, including the hypothesis that “the apple is delicious”

    peace

  18. fifthmonarchyman: I would not expect you to understand things like the law of noncontrdiction

    From our comments, you should be able to gather we do understand the law of non-contradiction. Because you *define* subjective and objective as a neat dichotomy, if something is subjective it can’t be objective, and if something is objective, it can’t be subjective. However, in science, objective has a meaning as an ideal that can be approached through a process of independent verification. For whatever reason, you seem to reject this sense of the word.

    fifthmonarchyman: You are ……still not getting it. I think “The apple is delicious” and think “This is an apple” are equally subjective.

    Yes, we understand your position.

    fifthmonarchyman: All you can independently verify is that conditions consistent with the hypothesis that “this is an apple” seem to exist.

    Independence generally means multiple observers, with differing perspectives, and with various methodologies. This is as opposed to the statement “The apple is delicious,” which is just an opinion of the apple that changes with each taster.

    fifthmonarchyman: the hypothesis that “the apple is delicious”

    There’s no way to independently verify the apple is delicious. Different observers may have different opinions.

  19. Zachriel: However, in science, objective has a meaning as an ideal that can be approached through a process of independent verification.

    ^^^^^^^^^^^^^^
    This!!!!!!!!!!!!!!!

  20. newton,

    But he cannot demonstrate revealed truth, and he remains limited by his being a simple human being. A mere claim doesn’t make his foundation anything but imaginary, giving him nothing but confidence in his imagined revelation (I’m leaving aside that, when examined carefully enough, his supposed foundations are absurd).

    You guys concede too much. Shouldn’t a proper skeptic reject those scenarios, like matrix/brain-in-a-vat, the very same way we reject claims about gods? If someone thinks that they’re a brain in a vat, then they’re welcome to it. Nothing will convince them otherwise (not even claims about gods and revelation, they’d use those as even more convincing evidence that they’re brains in a vat). If they want to convince me that we’re brains in a vat, however, they’d need evidence.

    Gods as solutions to solipsism? No, sorry, gods talking to you and revealing things to you would be reasons to suspect that you’re in trouble, not that you found a solution to a problem I don’t buy into in the first place.

    Anyway, one of the funniest thing about FMM’s position, as with any other presuppositionalist, is that where-the-rubber-meets-the-road, they show that they’re just as limited as any other human being. All those grandiose claims about their superior philosophy, only to fail where they should be showing how all of that bullshit helps.

  21. Entropy: gods talking to you and revealing things to you would be reasons to suspect that you’re in trouble, not that you found a solution to a problem I don’t buy into in the first place.

    You are still trying to make this a human endeavor.

    It’s not about you “finding a solution”. Trying to “find a solution” is what got you in this mess in the first place

    It’s about passively recognizing what you already know. What has been graciously done for you.

    and you are in trouble,

    You are a social creation who has purposely separated himself from the primary relationship you were created for.

    That is a heck of a predicament and there is no way for you to escape it by your own effort. The logical thing to do is surrender and beg your creator for mercy.

    but you won’t do that.

    Instead you will continue to try and find a solution all alone by yourself in your own head.

    peace

  22. Alan Fox: However, in science, objective has a meaning as an ideal that can be approached through a process of independent verification.

    I have no problem with science using an obscure idiosyncratic definition for objective.

    In that case the argument that

    “Special creation would not produce the objective nested hierarchy that we see”

    Is based on a blatant equivocation.

    peace

  23. Entropy: But he cannot demonstrate revealed truth…

    So? Is it true that he ought to be able to demonstrate revealed truth, and who revealed that to you?

  24. fifthmonarchyman: “Special creation would not produce the objective nested hierarchy that we see”

    But this isn’t the claim. The claim is Special Creation could produce any scenario we might observe. There are no entailments.

  25. Mung: Is it true that he ought to be able to demonstrate revealed truth, and who revealed that to you?

    Well, I don’t think he can. I think he’s in the same boat as everyone else.

  26. Alan Fox: But this isn’t the claim.

    Sure it is. look back at the beginning of this conversation.

    That is exactly what John harshman claimed.

    He even said that the only thing that would make him entertain the idea of special creation would be a lack of an objective nested hierarchy.

    That is the entire reason that I chose to comment on this thread

    peace

  27. fifthmonarchyman: Sure it is.

    I’m pretty sure it isn’t.

    look back at the beginning of this conversation.

    Provide a link, please.

    That is exactly what John harshman claimed.

    I’m sure John can speak for himself when he has an opportunity.

    He even said that the only thing that would make him entertain the idea of special creation would be a lack of an objective nested hierarchy.

    Well, I can see that. That’s not the same as saying “Design” claims are scientifically unentailed – untestable. If you could produce a hypothesis that ruled out a nested hierarchy, I’d be impressed. Maybe John would too.

    That is the entire reason that I chose to comment on this thread

    peace

    I’m skeptical! 🙂

  28. fifthmonarchyman: That is exactly what John harshman claimed.

    He even said that the only thing that would make him entertain the idea of special creation would be a lack of an objective nested hierarchy.

    I do claim that we expect common descent to show an objective nested hierarchy, by which I mean one that exists in the world to be discovered, independent of our prejudices and biases. And that various other things that have been categorized do not display such a hierarchy despite FMM’s attempt to make everything the same. And that we are indeed capable of discovering objective facts about the world by examining the world.

    Finally, I do claim that we would not expect a nested hierarchy of life to result from separate creation of species by an omnipotent being unless that being were attempting to convince us of common descent.

    There followed vast clouds of equivocation and obfuscation on FMM’s part, to no profit whatsoever. I expect nothing else in the future.

  29. Alan Fox: Well, I can see that. That’s not the same as saying “Design” claims are scientifically unentailed – untestable.

    This thread is about common decent verses special creation.

    There are no “design claims” at issue here.

    peace

  30. fifthmonarchyman: The reason we recognize human artifacts as “designed” is because we recognize similarities with archetypal design in creation.

    And yet many 8-year-old children can readily distinguish between designed objects and natural objects.

  31. Alan Fox: Provide a link, please.

    quote:

    We expect to see a nested hierarchy from common descent. We have no expectation of nested hierarchy from any other cause. Thus nested hierarchy is evidence of common descent.

    end quote:

    from here

    http://theskepticalzone.com/wp/promiscuous-domains-and-motifs-are-better-explained-by-common-design-than-common-descent-sals-module-hypothesis/comment-page-5/#comment-232346

    quote:
    Special creations of systems will not create nested hierarchies unless whoever creates them makes a particular point of creating a hierarchy for no necessary purpose.
    end quote:

    from here
    http://theskepticalzone.com/wp/promiscuous-domains-and-motifs-are-better-explained-by-common-design-than-common-descent-sals-module-hypothesis/comment-page-5/#comment-232358

    quote:
    That’s because you have no understanding of the difference between arbitrary nested hierarchies and nested hierarchies that result from hierarchical structure of the data. Some sorts of data actually do have such structure, and it can be objectively demonstrated that they do. That’s true for phylogenetic data, but it isn’t true for modes of transportation, musical instruments, etc. Would you agree that if what I say here is true, then what you said is wrong?
    end quote

    from here
    http://theskepticalzone.com/wp/promiscuous-domains-and-motifs-are-better-explained-by-common-design-than-common-descent-sals-module-hypothesis/comment-page-5/#comment-232360

  32. John Harshman: Finally, I do claim that we would not expect a nested hierarchy of life to result from separate creation of species by an omnipotent being unless that being were attempting to convince us of common descent*

    @FMM

    Clearer now?

    *My emphasis.

  33. fifthmonarchyman:
    You won’t be surprised to know that I think you have it exactly backward.

    I’ve been reading ID-creationist claims for quite a while, and they talk about this as if it were really scientific, all based on what we know about design from our own activities. But I appreciate your honesty in revealing, directly, that it’s all religious fanaticism/fantasy, rather than needing my help to figure out how a simple philosophical problem reveals it so. Your case, unlike the ID-creationists case, is much more open to its true “foundations.”

  34. Alan Fox: Clearer now?

    No what does your emphasis have to do with his contention that special creation will not be expected to produce an objective nested hierarchy?

    he said this after I showed him that anything whatsoever that can be categorized can be described as a nested hierarchy.

    peace

  35. Entropy: they talk about this as if it were really scientific, all based on what we know about design from our own activities.

    I don’t disagree that we know about design from our own activities.

    But our design activities are types of the archetypal design we see in nature.

    There is nothing unscientific about that realization.

    peace

  36. Entropy,

    You will be happy to know that I am right now trying to see if I can recognize the difference between algorithms and “design” in weather temperature measurements.

    Nothing about proving that God exists just practical ID in action.

    peace

  37. fifthmonarchyman,

    I suspect that you don’t understand what “a problem I don’t buy into in the first place” means. So much for that superior philosophy. Your god reveals things to you as poorly as if it were imaginary. How surprising.

  38. Alan Fox: Good grief! “unless … etc”!

    unless what exactly??

    He specifically said that the only way that he would entertain the idea of special creation is if life did not produce an objective nested hierarchy.

    If you are admitting that there is no way whatsoever that you would entertain special creation then fine.

    That is not John Harshman’s position.

    And it’s certainly not very scientific

    peace

  39. Entropy: I suspect that you don’t understand what “a problem I don’t buy into in the first place” means.

    Do you think it’s necessary for you to understand that you have a problem before you can have one.

    If so that explains a lot

    peace

  40. fifthmonarchyman: Do you think it’s necessary for you to understand that you have a problem before you can have one.

    Do you understand that your claiming so doesn’t mean that I have such a problem?

    More importantly, do you understand that if I say that I don’t buy into it, it means that I’m not looking for a solution, as you claimed that I was?

    So much for that superior philosophy. Your god reveals things to you as poorly as if it were imaginary. How surprising.

  41. Entropy,

    thus revealing the quality of your imaginary friend’s “revelations

    Can you support the claim his friend is imaginary.

  42. colewd:
    Can you support the claim his friend is imaginary.

    I don’t need to. FMM does a very good job showing so all by himself.

    Why? Do you, like FMM, get revelations, supposedly from an all-powerful omniscient being, that are, however, indistinguishable from the imagination of a not-that-bright individual?

  43. Zachriel: It does for those who reject your solipsism

    fifthmonarchyman: I’m not a sophist. Far from it. I think that sophism or absurdity is the necessary result of any worldview that consistently rejects God.

    WTF?

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