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

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

  1. John Harshman: No. Talking to you is generally a useless exercise.

    no worries

    I hope you have a great day.

    John Harshman: Let’s just say that you know nothing about this

    You can say that all you want but with out elaboration it rings a little hollow.

    😉

    peace

  2. fifthmonarchyman: OK, I never said otherwise. It has nothing to do with this discussion.

    You on the other hand while discussing my scenario said

    quote:”bring in a scientist, take some DNA samples and you’ll get the right (objective & discoverable) family tree every time.
    end quote:

    I hope you realize now that that is clearly incorrect.

    peace

    If I didn’t know you I would think you’re kidding me. Pathetic dude, pathetic

  3. Rumraket: Mung now seems to be saying that what he intended to ask was how one can know, from looking at the genes of two individuals, that they are bothers.

    I can spot bothers without looking at their genetics. 🙂

  4. John Harshman: I missed that too.

    here it is

    quote:

    “Species” are irrelevant to this discussion.

    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-7/#comment-232653

    and here

    quote:

    The terminal nodes in a tree of DNA sequences are sequences taken from individuals. We common consider the individuals as exemplars of their species, but one can make trees with many individuals from the same species, or individuals claimed to belong to the same species, and this is frequently done. No assumption that the nodes represent species is necessary. You don’t know what you’re talking about.

    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-8/#comment-232672

    peace

  5. Mung: Yet imagination seems to substitute just fine as knowledge for Darwinists. Go figure.

    I don’t know any Darwinists, so I don’t know if you’re right or wrong about them. I know lots of creationists though, and for creationists imagination substitutes just fine for knowledge.

  6. John Harshman: None of that means what you imagine it does.

    I “imagine” you chastised me for focusing on species and rightly pointed out that the nested hierarchy ends with individuals. …………

    So you are saying that you did not chastise me for focusing on species and rightly point out that the nested hierarchy ends with individuals??

    peace

  7. fifthmonarchyman: I noticed you added the qualifier “methodologically”.

    Yes of course, because that’s what actually matters. It is completely irrelevant whether scientists doing the work are already convinced that common descent is true, what matters is whether they’re doing their investigations correctly or not.

    If the different phylogenetic trees are not methodologically biased towards particular outcomes, then the personal beliefs of the scientists are irrelevant.

    The claim is that there is a statistically significant level of corroboration between independent phylogenetic trees on a common topology. And that this result is not a product of someone forcing them to be similar. That they ARE similar. And that is a fact that needs to be explained. Why WOULD they be similar? There’s an immediate explanation for that: they share a common genealogy. And there is no other good reason for that.

    Now you come along and say something to the effect that the result, that independent sets of data are found to agree on a common topology, is somehow the result of a kind of “process bias” among scientists doing peer review.

    Prove it.

    If you assume common decent while categorizing and look for “the correct evolutionary branching” you will come up with a tree that is consistent with common decent.

    What does that even mean? What are you saying happens in practice? A scientist picks a gene from several different species of primates (say), then infers a phylogeny. Then picks another gene from the same handful of species, infers a new phylogeny. Then she compares them, and if they don’t agree to a statistically significant extent, then… what? She forces them to? She ignores it? Or what? Be specific, give examples.

    If different folks do this and then compare their trees trying to come up with the one true tree using a peer reviewed process eventually there will be a convergence with any outliers being ignored and their proponents excluded from discourse.

    Get specific, show this purported data that scientists are ignoring. I suggest we take a look at primates. I invite you to show how there actually isn’t any consilience of independent phylogenies for primates.

    This honestly just looks like some ad-hoc excuse you are concocting to try to dismiss the evidence of consilience of independent phylogenies. Stop this vague handwaving and put your money where your mouth is so to speak.

  8. Rumraket: It is completely irrelevant whether scientists doing the work are already convinced that common descent is true, what matters is whether they’re doing their investigations correctly or not.

    We weigh the data as individuals not as “methods”.

    Subjectivity is about persons. Methods can’t be subjective because they are not persons. You can’t have science without scientists.

    Methods aren’t people they don’t build trees. Scientists build trees using methods as tools

    It’s people who choose whether this or that character is of greater or lessor importance.

    “Methods” are impotent and ineffectual with out people to use them and choose the inputs and evaluate the outputs.

    Rumraket: If the different phylogenetic trees are not methodologically biased towards particular outcomes, then the personal beliefs of the scientists are irrelevant.

    The data forms trees that are consistent with common decent simply because trees that aren’t would never occur to folks who assume common decent.

    Rumraket: Now you come along and say something to the effect that the result, that independent sets of data are found to agree on a common topology, is somehow the result of a kind of “process bias” among scientists doing peer review.

    It’s not a “process bias”. People will just naturally be more drawn to ideas they can agree with. That should not be controversial. It’s just common sense.

    Peer review is not infallible because it is dependent on human beings.

    https://www.forbes.com/sites/geoffreykabat/2015/11/23/the-crisis-of-peer-review/#28fcab1e463e

    http://journals.sagepub.com/doi/pdf/10.1177/014107680609900414

    Rumraket: I suggest we take a look at primates. I invite you to show how there actually isn’t any consilience of independent phylogenies for primates.

    I agree there is consilience. That is what you would expect when everyone agrees that there is one unique tree to be found

    I don’t think that a truly independent phylogeny that radically contradicted those we already have could ever be accepted. Despite that we see large changes to the accepted tree all the time. At the largest scales It looks very different than it did even a few decades ago

    I already offered a couple of independent categorizations that don’t mesh with the linnaean tree.

    One of them is my own construction that focused on readily observable features like color and habitat and habit and another that grouped animals according to the niches associated with them. In either of these schemes linnaean groupings like “primates” are beside the point.

    Rumraket: This honestly just looks like some ad-hoc excuse you are concocting to try to dismiss the evidence of consilience of independent phylogenies.

    I don’t dismiss anything.

    You keep forgetting that I don’t reject common decent. I just don’t think that consilience among groupings constructed to reflect an assumed single true tree means what you seem to think it means.

    peace

  9. fifthmonarchyman,

    Everything that you write here is delightfully wrong.
    Firstly, I believe the *vast* majority of phylogeny done these days is molecular; the method consists of taking the sequences of homologous genes from multiple organisms and feeding them into a computer program. The computer program constructs a tree that (typically, by way of example) constructs the most parsimonious tree for that set of sequences. It does this without knowledge of which sequences come from beasts with fur, which with scales, which with exoskeletons, etc.
    The reality-based posters’ point here is that when you repeat this exercise with different sets of genes, you get the same effing tree. There are (and you can model this and show that it is the expected result) very minor differences between the trees. By and large, the trees match. They match in a way that is billions of billions of times more likely under common descent than under other scenarios.
    Secondly, and this is the error that makes me laugh out loud, the Darwinist omerta does not work the way you think it does. In the 1990’s, I cloned the human phospho-enol pyruvate carboxykinase gene. Suppose I sequenced it, and compared human PEPCK with the PEPCK sequence from a whole pile of other species, running a phylogenetic analysis.
    Creationists think that if my analysis showed that humans were closely related to crickets, not bonobos, then I would not be able to publish my results (Darwinist omerta), but if, otoh, the computer program said that humans were closest to bonobos, close to sheep and distantly related to crickets and trypanosomes, then I would have no difficulty getting published.
    Pay attention now:
    The. Reverse. Is. True.
    Results that confirm what we already believed was true bore scientists. Results that overturn the current paradigm get the top journals competing to publish them, and win prizes for their authors.
    The drive to consilience comes from the data, not the researchers. In fact, you only hear about the exceptions, because that’s what interests scientists.
    You have it backwards. That’s funny.

  10. fifthmonarchyman: You must have missed the comment in this very thread where John Harshman chastised me for focusing on species. He rightly pointed out that the nested hierarchy ends with individuals.

    peace

    Actually, the nested hierarchy ends with the DNA of individuals. Cells have a hierarchy too.

  11. I’d like to know the process by which the consensus view is arrived at, if not by data. If there is some shadowy protector of the True Tree, how do they enforce this view? No-one ever sidled up to me when I was at Uni and told me which way my research should go, with bribes or threats.

  12. stcordova:
    I’ve been trying work my way through protein families.

    What is the prevailing view about universal common ancestry of PROTEINS vs. organisms. Did all extant proteins descent from some single universal protein, or were there independent origins of proteins?

    Thanks in advance.

    A mixture, I think. The question could be rephrased: did the DNA in a taxonomically restricted protein come from protein coding or noncoding sequence? It’s unlikely that a folded, functional catalytic long protein could come entirely from DNA which has never coded for protein – not even a pseudogene. But small modules are fairly easy. There are billions of random short sequences that would make a segment of alpha helix, for example. Conversely, there are a lot of alpha helixes already in proteins.

    Of course this argument applies only to organisms with large amounts of noncoding DNA, such as our self-regarding selves. For prokaryotes, there’s not much choice: stick a thumb in the genome and your plum is a protein segment most of the time.

  13. Allan Miller: If there is some shadowy protector of the True Tree, how do they enforce this view?

    It’s not that there is a person out there who is enforcing their view on others. Everyone is just going about their business doing the best they can with the information they have.

    Everyone already knows there is a True Tree so that any data that is in conflict with that obvious knowledge is assumed to be noise.

    If there are two trees that each claim to be the True Tree then folks will weigh the evidence and decide which claim seems more likely and which one must be mistaken in some way.

    There is nothing conscious or malicious about it it’s just the way we humans make sense of our world.

    There is nothing at all wrong with this approach it’s just not “objective” and like anything else it relies on the validity of the underlining assumptions that are brought into it.

    peace

  14. DNA_Jock: The computer program constructs a tree

    computer programs are not persons they don’t construct trees. People construct trees while using computer programs as tools to help them. Parameters must be chosen, input data must be entered, appropriate sampling methods must be chosen, results must be crosschecked for accuracy against other samples.

    All of this is done by humans. There is no way to do science with out scientists.

    DNA_Jock: There are (and you can model this and show that it is the expected result) very minor differences between the trees. By and large, the trees match.

    Terms like “very minor” and “by and large” are subjective value judgements. They are the kind of thing you can only get with human judgement.

    DNA_Jock: Creationists think that if my analysis showed that humans were closely related to crickets, not bonobos, then I would not be able to publish my results

    No,

    You would never conclude that your analysis showed that humans were closely related to crickets, not bonobos in the first place. You would conclude that you had made a mistake or you were looking at the wrong data.

    It’s just the way that we humans work we don’t even see information that radically contradicts what we already know to be true. This is not a smear against you. Life would be impossible if we began every single task with a blank slate.

    DNA_Jock: The drive to consilience comes from the data, not the researchers.

    Again data is not a person it doesn’t drive.

    Data is collected and weighted and evaluated by humans. In this case it’s done by humans that KNOW that there will be consilience if they are doing it right.

    Again there is nothing at all wrong with any of this. It’s just how things are.

    peace

  15. DNA_Jock: Results that overturn the current paradigm get the top journals competing to publish them, and win prizes for their authors.

    I completely agree. but in order for this to happen we have to be able to make sense of the results we see. We need to be able to contextualize them into the larger framework of our knowledge of the world.

    To a person that KNOWS something a contradictory result just looks like a mistake or noise.

    We KNOW that organisms don’t spontaneously appear out of nowhere so that any “result” that suggests that this is what happened must be in error. We would never give it a second thought

    A great example of this sort of thing is the “discovery” of dark matter.

    We KNOW that gravity acts in a certain way and when we see data that contradicts what we know we simply postulate hidden matter to account for the discrepancy in our measurements.

    peace

  16. fifthmonarchyman: You would never conclude that your analysis showed that humans were closely related to crickets, not bonobos in the first place. You would conclude that you had made a mistake or you were looking at the wrong data.

    It’s just the way that we humans work we don’t even see information that radically contradicts what we already know to be true. This is not a smear against you. Life would be impossible if we began every single task with a blank slate.

    More insulting bullshit from you.
    Not everyone is like you, some people care for what’s true instead of reassuring themselves in their ridiculous presuppositions

  17. dazz: Not everyone is like you, some people care for what’s true instead of reassuring themselves in their ridiculous presuppositions

    I deeply care about what is true. It’s the most important thing my my life.

    The difference is that I realize that I’m not God.

    As a subjective finite human the only way for me to ever get to the objective truth is for it to be revealed to me.

    peace

  18. Are all proteins phylogenetically descended from a single protein. If one argues for nested hierarchies, then what about the nested hierarchy of proteins. What do people believe about the “LUCA” of protein. Did it ever exist. Or were the major families of proteins independently evolved.

    If someone already gave their opinion, apologies.

  19. The reason I’m posing the problem, I’ll be shortly learning pFAM, and what little exposure I got to protein taxonomies ever suggested there was one unifying protein architecture. This is, imho brutally obvious if you compare the following 2 protein architectures. Here is the KRAB-ZNF architecture:

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