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

  1. fifthmonarchyman
    Ignored
    says:

    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. Mung Mung
    Ignored
    says:

    John Harshman: …and your imagination is no substitute for actual knowledge.

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

  3. dazz dazz
    Ignored
    says:

    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

  4. Mung Mung
    Ignored
    says:

    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. 🙂

  5. fifthmonarchyman
    Ignored
    says:

    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

  6. fifthmonarchyman
    Ignored
    says:

    Mung: I can spot bothers without looking at their genetics. 🙂

    Is your observation objective? 😉

    peace

  7. John Harshman John Harshman
    Ignored
    says:

    fifthmonarchyman: here it is

    None of that means what you imagine it does.

  8. Entropy Entropy
    Ignored
    says:

    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.

  9. fifthmonarchyman
    Ignored
    says:

    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

  10. Rumraket Rumraket
    Ignored
    says:

    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.

  11. fifthmonarchyman
    Ignored
    says:

    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

  12. DNA_Jock
    Ignored
    says:

    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.

  13. Allan Miller
    Ignored
    says:

    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.

  14. Allan Miller
    Ignored
    says:

    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.

  15. Allan Miller
    Ignored
    says:

    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.

  16. fifthmonarchyman
    Ignored
    says:

    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

  17. fifthmonarchyman
    Ignored
    says:

    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

  18. fifthmonarchyman
    Ignored
    says:

    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

  19. dazz dazz
    Ignored
    says:

    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

  20. fifthmonarchyman
    Ignored
    says:

    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

  21. stcordova
    Ignored
    says:

    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.

  22. stcordova
    Ignored
    says:

    Allan,

    Thanks for your answer.

    Sal

  23. stcordova
    Ignored
    says:

    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:

    Click to ENLARGE

  24. stcordova
    Ignored
    says:

    Top2 domains. What I’m trying to point out is the absurdity of saying there is a nested hierarchy that goes to universal common ancestor of all proteins. Not that anyone is saying such a thing, BUT, since phylogenists keep advertising protein phylogenies, they keep avoiding the poofomorphies needed to make new protein architectures. It doesn’t obey smooth phylogenetic evolution:

    Click to ENLARGE

  25. John Harshman John Harshman
    Ignored
    says:

    Sal, my advice: think more about what you want to say before you post. So far we have a stream of consciousness with pretty pictures. I even think there are important words missing; for example, when you say “what little exposure I got to protein taxonomies ever suggested there was one unifying protein architecture”, I suspect you actually meant the opposite. As for your claims of “poofomorphies”, you have no evidence for any such thing.

  26. stcordova
    Ignored
    says:

    John,

    You’re the one helping my thought process, so I just say what’s on my mind to see if you have something of substance in my critique of UCA.

    You could actually address the problem posed. Can you build a phylogeny of proteins all the way to a universal common ancestor of proteins. If not, it serves as an example of why the assumption of universal common ancestry is utterly useless.

    Thanks any way for responding.

  27. DNA_Jock
    Ignored
    says:

    fifthmonarchyman,

    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.

    True. But the fact that I use a subjective value judgement to communicate with you does NOT make the underlying data any less objective. Were you numerate, you could check it out.

    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.

    Delightfully wrong, as ever. I WOULD conclude that my analysis showed humans were closer to crickets. I would, based on background knowledge, conclude that something else was going on here. I would not discard the data as noise, I would try to figure out what was going on.

    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.

    Experimental scientists are quite used to having their confirmation bias bite them in the ass on a daily basis. They therefore learn to minimize it. Internet theologians, otoh…

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

    To an experimental scientist, “Huh, that’s wrong!” and “WTF! That’s weird!” are the jumping off points for career-defining and prize-winning research. Learn about the history of science.

    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.

    That’s right, and when astronomers found irregularities in the orbit of Uranus, they postulated an unidentified planet to explain it…
    They did NOT say, “oh that’s noise, let’s ignore it.” They went looking.
    Great example.

  28. stcordova
    Ignored
    says:

    John,

    Look at the two architectures KRAB-ZNF protein family vs. Top2A, what’s the evidence they came from an ancestral protein. Like none? Agree.

  29. dazz dazz
    Ignored
    says:

    DNA_Jock: That’s right, and when astronomers found irregularities in the orbit of Uranus, they postulated an unidentified planet to explain it…
    They did NOT say, “oh that’s noise, let’s ignore it.” They went looking.
    Great example.

    FMM and his self defeating examples. Hahahaha. Poor clueless hack

  30. stcordova
    Ignored
    says:

    DNA_Jock:

    when astronomers found irregularities in the orbit of Uranus, they postulated an unidentified planet to explain it…

    So what phenomenon, IN PRINCIPLE, might be required to postulate “God Did It?”

  31. dazz dazz
    Ignored
    says:

    stcordova: Can you build a phylogeny of proteins all the way to a universal common ancestor of proteins. If not, it serves as an example of why the assumption of universal common ancestry is utterly useless.

    Typical creationist logic fail. SMFH

  32. fifthmonarchyman
    Ignored
    says:

    DNA_Jock: But the fact that I use a subjective value judgement to communicate with you does NOT make the underlying data any less objective.

    Data is not objective or subjective its just………. data
    Our interpretations of the data is where our subjectiveness enters the picture.

    DNA_Jock: Were you numerate, you could check it out.

    I could check out your math but I could not check out the underlying intentions and biases that were involved in the decision to use this data rather than some other data.

    I could look at your conclusions and agree with your “very minor” and “by and large” adjectives. That would not make your conclusions objective and it would not make your characterization correct.

    DNA_Jock: I would, based on background knowledge, conclude that something else was going on here.

    That is what I thought I said. You would decide that you were looking at the wrong data to determine an evolutionary relationship. or something else.

    You would not conclude that humans were closely related to crickets. That is the point

    DNA_Jock: I would try to figure out what was going on.

    Right, You would try to contextualize your observations and harmonize them with what you KNOW to be true.

    This includes the knowledge that humans are more closely related to chimps than crickets

    DNA_Jock: They therefore learn to minimize it.…

    We all try and minimize it. Minimizing is not the same thing as eliminating. We can do the former to some extent but will never be able to do the later.

    Because we are humans and not machines

    DNA_Jock: “Huh, that’s wrong!” and “WTF! That’s weird!” are the jumping off points for career-defining and prize-winning research.

    Again I completely agree. The problem is you can only get to “that’s weird” from a framework of what you already know to be true.

    If you don’t make assumptions nothing is weird and nothing is normal.

    DNA_Jock: That’s right, and when astronomers found irregularities in the orbit of Uranus, they postulated an unidentified planet to explain it…

    Exactly my point because they knew that Uranus should orbit in a certain way they looked for an explanation with in the context of what they already knew.

    They did not conclude that they wrong about the way that Uranus should orbit the sun.

    You are literally making my point for me.

    peace

  33. dazz dazz
    Ignored
    says:

    stcordova: So what phenomenon, IN PRINCIPLE, might be required to postulate “God Did It?”

    Who’s to blame for your failure to produce any kind of scientific explanation based on god?

  34. OMagain
    Ignored
    says:

    stcordova: So what phenomenon, IN PRINCIPLE, might be required to postulate “God Did It?”

    Sal,
    Humanity started out with that as a given. Did you skip history class?

    The reason we’re able to discuss these matters at all on these “computers” is because “god did it” was an insufficient explanation for some.

  35. Rumraket Rumraket
    Ignored
    says:

    stcordova:
    Are all proteins phylogenetically descended from a single protein.

    Is that a question? You need question marks.

    The answer is no.

    If one argues for nested hierarchies, then what about the nested hierarchy of proteins.

    There is no single nested hierarchy of all proteins. There are nested hiearchies of different protein families and superfamilies.

    What do people believe about the “LUCA” of protein.

    That there was no such thing.

    Or were the major families of proteins independently evolved.

    Mostly yes, that is the current view based on the evidence.

  36. stcordova
    Ignored
    says:

    dazz, OMagain,

    I asked, HYPOTHETICALLY, what event or phenomenon (if you saw it or found it or encountered it somehow) would be so far out of natural expectation that you’d say, “God did it.” If you there is nothing like that in principle, then well, nothing will convince you. That’s ok, I was just asking you to be up front about.

    As far as the OP is concerned, I’m arguing the problem of promiscuous domains is sufficient for me to believe, “God did it.” Maybe not you, and I respect that. But I was just trying to get you guys to admit nothing would ever convince you of some Deity, much less the Christian one.

  37. Zachriel Zachriel
    Ignored
    says:

    fifthmonarchyman: Exactly my point because they knew that Uranus should orbit in a certain way they looked for an explanation with in the context of what they already knew.

    That eventually worked for Uranus, but not for the anomalies in the precession of the perihelion of Mercury’s orbit. They checked and rechecked their observations. The finding was independently verified (scientific objectivity). They searched for solutions within the prevailing paradigm, but that pursuit was fruitless. The answer had to wait for a new theoretical paradigm.

    “They did NOT say, ‘oh that’s noise, let’s ignore it.’ They went looking.”

  38. Rumraket Rumraket
    Ignored
    says:

    stcordova: So what phenomenon, IN PRINCIPLE, might be required to postulate “God Did It?”

    A model of “God creating” that gives testable mechanisms, and reasons that lead to quantifiable expectations. As in something we should expect to be the case if God does it, because we have some reason (that isn’t just ad-hoc dreamt up and retro-fitted to known data) to think that that is what God would do.

    If IDcreationists who think God Did It can’t come up with such a model, that is not a failure of-or indication that science is biased against God, rather that is an indication of the worthlessness of the “God-hypothesis”.

  39. stcordova
    Ignored
    says:

    sal:
    Or were the major families of proteins independently evolved.

    Rumraket:

    Mostly yes, that is the current view based on the evidence.

    WHOA! The nested hiearchies of proteins don’t point to a universal common ancestor! So nested hierarchies don’t have to point to a universal common ancestor.

    https://media.giphy.com/media/LBoGw27rM34aY/giphy.gif

  40. stcordova
    Ignored
    says:

    Rumraket:

    A model of “God creating”

    What if God cannot be reduced to repeatable mechanistic descriptions (like the laws of physics), would there be a gap you believe in such a God? If not, I respect that, but I’m just pointing out, if the mechanism is undefinable you might not believe it. However, that doesn’t seem to stop you from believing in evolutionary mechanisms and abiogenetic mechanisms that you’ve yet to describe.

    You don’t really know they exist either, and for all we know they may be undiscoverable. So you believe in the unknown the undiscoverable despite lack of mechnaistic description. You BELIEVE BELIEVE BELIEVE without knowing. Ok, you’re not that much different from the creationist whom you despise.

  41. newton
    Ignored
    says:

    fifthmonarchyman:

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

    What we discovered is according to our present understanding of the universe the mass of galaxies is not enough to keep them from flying apart when they rotate. We didn’t know that and now we do.

    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.

    We have good reasons to think we understand the parameters of gravity, we are able to calculate it well enough to send spacecraft to distant planets.

    So faced with the discrepancy ,various hypothetical answers have been proposed. One is our present understanding is incorrect.

    If revelation is the only source of discovery and knowledge , how would you use it to resolve the dilemma? Were we mistaken about gravity because of misunderstanding earlier revelation or is the discrepancy the result of misunderstanding revelation?

    peace

  42. Rumraket Rumraket
    Ignored
    says:

    stcordova: WHOA! The nested hiearchies of proteins don’t point to a universal common ancestor!

    LOL, this is news to you?

    Have you learned absolutely nothing over the last few years?

    There are protein trees that point to a universal common ancestor, it’s just that not all proteins can be traced to that universal ancestor. Many proteins have arisen subsequently in different clades and therefore can only be used to infer the common descent of that particular clade.

    So nested hierarchies don’t have to point to a universal common ancestor.

    Correct. Common descent is not contingent on it having to be the case that all possible protein trees can be traced to the last universal ancestor. Proteins that arose in clades that emerged subsequently to LUCA obviously should not be traceable that far back.

    A protein that arose around the time of the last universal primate ancestor, for example, will obviously not be able to corroborate the common descent of all life, but only the primate clade in which it is found.

    How can this be surprising to you? You have obsessed repeatedly about so-called ORFan genes and taxonomically restricted genes. Now seemingly unaware of what the hell that even means.

    Did you somehow pull a Bill Cole and suffer an involuntary cognitive “reset” recently? Do you understand ANY of this? At all?

  43. Alan Fox Alan Fox
    Ignored
    says:

    stcordova: What if God cannot be reduced to repeatable mechanistic descriptions (like the laws of physics), would there be a gap you believe in such a God?

    How could a God not be irreducible to physical laws? That seems to be the essence of a God. Gods’s creation, on the other hand – the Universe – may be. When I make that distinction, it seems God can only intervene using the laws of the universe with which he imbued it. How that works? Beats me! 😯

  44. dazz dazz
    Ignored
    says:

    stcordova: What if God cannot be reduced to repeatable mechanistic descriptions

    Well, that’s your problem, not ours. You’ve been told countless times that classical theists hold that that’s impossible to do, and your attempts to find signs of divine intervention in particular natural events or natural phenomena are bound to fail. If you agree with them that God can’t be reduced to mechanistic processes, you should ask yourself why you keep wasting your time with all that “creation science” crap.

  45. stcordova
    Ignored
    says:

    Alan Fox: How could a God not be irreducible to physical laws? That seems to be the essence of a God. Gods’s creation, on the other hand – the Universe – may be. When I make that distinction, it seems God can only intervene using the laws of the universe with which he imbued it. How that works? Beats me! :O

    My answer to your question was explored here in response to something VJ Torley said:

    https://uncommondescent.com/intelligent-design/cavin-and-colombetti-miracle-debunkers-or-can-a-transcendent-designer-manipulate-the-cosmos/#comment-482044

  46. stcordova
    Ignored
    says:

    dazz:

    dazz: Well, that’s your problem, not ours. You’ve been told countless times that classical theists hold that that’s impossible to do, and your attempts to find signs of divine intervention in particular natural events or natural phenomena are bound to fail. If you agree with them that God can’t be reduced to mechanistic processes, you should ask yourself why you keep wasting your time with all that “creation science” crap.

    So I take it to mean you won’t believe in a God you cannot completely explain in terms of repeatable experiments and laws derived from repeatable experiments. Is that right.

    That’s your problem, not ours.

    Actually it’s your problem. How can you know anything absolutely except your own pain, because the only certainty is pain? You can only guess and believe what is ultimately true.

  47. Rumraket Rumraket
    Ignored
    says:

    stcordova: What if God cannot be reduced to repeatable mechanistic descriptions (like the laws of physics), would there be a gap you believe in such a God?

    Then you have a problem, because how could you have evidence of an inscrutable mechanism if it cannot even in principle lead to a prediction? Then your “scientific creationism” nothing but hot air and flailing. But we already knew that.

    If not, I respect that

    I don’t. I don’t respect that. I think it’s idiotic. A person cannot have good scientific reasons for believing in an in principle untestable mechanism. You would basically just have to believe on nothing but blind, fevered, delusional faith. It would be nothing but make-believe. A wish, a desire, a hope. But with zero to show for it.

    but I’m just pointing out, if the mechanism is undefinable you might not believe it.

    I agree. Which is why I don’t believe in creationism.

    However, that doesn’t seem to stop you from believing in evolutionary mechanisms and abiogenetic mechanisms that you’ve yet to describe.

    I have seen loads of evolutionary and abiogenetic mechanisms described. Scientists are performing experiments, and comparing the predictions of mechanistic models with observations of newly collected data as we speak.

    You don’t really know they exist either, and for all we know they may be undiscoverable.

    Be specific. What is “they” that might be undiscoverable? And what is it in particular you think I believe without a testable mechanism or evidence?

    So you believe in the unknown the undiscoverable despite lack of mechnaistic description. You BELIEVE BELIEVE BELIEVE without knowing. Ok, you’re not that much different from the creationist whom you despise.

    First of all, I have to note here that you concede my main point, that your position is essentially make-believe(after all you say I’m supposedly not htat much different from the creationsists, and since you’re accusing me of just believing in the uknowable, that must by implication be what you’re doing). So it is YOU why just BELIEVE BELIEVE BELIEVE without knowing, and I’m glad you can at least in some sense admit to that.

    Second, I don’t. I don’t believe in untestable models of evolution or abiogenesis. In so far as it is unknowable or untestable, I don’t believe it, I just admit to not knowing. That’s it. But you seem to be different, and can’t seem to exist without having something to cling to and believe. Well that’s not my problem, that’s yours. All I can say is that mere belief for it’s own sake is not a reliable path to truth, and I’d rather just abstain from forming beliefs in cases where the truth of the matter can’t be probed, than to commit myself to a potential false positive or false negative for no good reason.

  48. stcordova
    Ignored
    says:

    Rumraket:

    LOL, this is news to you?

    Have you learned absolutely nothing over the last few years?

    Well, I learned something today. Yay!

  49. Rumraket Rumraket
    Ignored
    says:

    stcordova: Well, I learned something today.Yay!

    So you admit to not having had even the faintest clue what a taxonomically restricted, or ORFan gene was, the last twenty times you used the term?

  50. Alan Fox Alan Fox
    Ignored
    says:

    stcordova,

    Following Sal’s link:

    If there is a God who designed the “laws”, we have laws because he is choosing to do things with a certain amount of regularity, but Belinfante rightly observes God at any time can choose to stop the universe from behaving in such regular manners. It would appear God had reasons for behaving in regular manners.

    ID sympathizers believe the reason he makes the universe behave in somewhat predictable ways is to make the universe comprehensible to humans. But there is nothing stopping God from changing his convention.

    Well that’s some powerfully wishful thinking there, Sal! But those changes should be observable. There should be discontinuity whenever God intervenes. Maybe he always intervenes when nobody’s looking. Could be. No way to tell, I guess. Still seems like looking through the wrong end of the telescope.

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