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:

    Corneel: everything is equally uncertain and equaly subjective to you

    No that is simply not true. I can be partially certain or somewhat certain.

    There is however no way that a person can be biased and unbiased at the same time in the same respect.

    Objectivity requires a lack of bias. A somewhat biased person can’t be objective. And finite persons can’t be totally unbiased. Nor would we want them to be our bias/perspective is what makes us persons in the first place as apposed to machines.

    I’m not saying that all opinions are equally subjective. You can’t quantify subjectivity you either are subjective or you are not. It’s binary and not analog.

    Your opinions might be less biased than everyone else and that certainly is a good thing in many situations but you can’t completely set aside your perspective on the world. It is simply impossible.

    Corneel: I did feel the need to seize the rare grayshaded bloom in the black-and-white desert.

    The blooms might be grey but they are blooms they are not partial rocks.

    Alan Fox: Shame you can’t make that final connection as to how paws and hands (and pandas’ thumbs) might have similarities that hint* at a hierarchy of relatedness.

    Again…………….
    I don’t deny common decent. I don’t reject the nested hierarchy.

    The fact that I have to repeatedly say that is evidence of bias and selective hearing in your interactions with folks who disagree with you.

    That is not a slam we are all biased and hear selectively it’s part of what makes us human.

    Although I don’t reject the nested hierarchy I do is reject the notion that the categorizations of human beings can be said to be objective.

    peace

  2. fifthmonarchyman
    Ignored
    says:

    OMagain: technology can ultimately extend lifespan near indefinitely

    Extending lifespan near indefinitely is not remotely the same thing as “curing death”.

    Living 1,000 or 10,000 or 10 trillion years is not living forever. Not even close.

    What is it about atheists that keeps them from understanding the concept of the excluded middle?

    Peace

  3. PeterP
    Ignored
    says:

    fifthmonarchyman: No that is simply not true. I can be partially certain or somewhat certain.

    Now that is funny!

    Partially certain is no different than being somewhat certain and being somewhat certain is akin to being partially certain. However, I’ll be charitable and ask you what the difference is betwixt the two?

    There is however no way that a person can be biased and unbiased at the same time in the same respect.

    Objectivity requires a lack of bias. A somewhat biased person can’t be objective. And finite persons can’t be totally unbiased. Nor would we want them to be our bias/perspective is what makes us persons in the first place as apposed to machines.

    folks are quite capable of setting their biases aside when necessary.

    I’m not saying that all opinions are equally subjective. You can’t quantify subjectivity you either are subjective or you are not. It’s binary and not analog.

    If you cannot quantify subjectivity then all opinions are equally subjective. As you state it is binary.

    I do is reject the notion that the categorizations of human beings can be said to be objective.

    Nonsense.

  4. fifthmonarchyman
    Ignored
    says:

    PeterP: However, I’ll be charitable and ask you what the difference is betwixt the two?

    Not necessarily any difference at all. The point was that there is something between certain and dubious. Why do you ask?

    PeterP: If you cannot quantify subjectivity then all opinions are equally subjective. As you state it is binary.

    No when you can’t quantify something that means that terms like “equal” have no meaning.

    Saying that nighttime is the opposite of daytime does not mean that 8 PM and 1 AM are equal. It just means neither is daytime and they never can be daytime .

    PeterP: Nonsense.

    Does that mean that you agree that humans can’t be completely impartial or does it mean that you think it’s nonsense to say that humans can’t be completely impartial?

    peace

  5. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: No that is simply not true. I can be partially certain or somewhat certain.

    About the big picture, but not about individual facts. That is what you said.

    fifthmonarchyman: There is however no way that a person can be biased and unbiased at the same time in the same respect.

    Objectivity requires a lack of bias. A somewhat biased person can’t be objective. And finite persons can’t be totally unbiased. Nor would we want them to be our bias/perspective is what makes us persons in the first place as apposed to machines.

    If we acknowledge that every observation of the world, no matter how mundane, is tainted by subjective bias, then we must also concede that complete certainty is unattainable.

    fifthmonarchyman: I’m not saying that all opinions are equally subjective. You can’t quantify subjectivity you either are subjective or you are not. It’s binary and not analog.

    Your opinions might be less biased than everyone else and that certainly is a good thing in many situations but you can’t completely set aside your perspective on the world. It is simply impossible.

    And you have been using that argument to dismiss unwelcome facts that happen to be backed up by mainstream science, like you did in your recent discussion with John, like you did in the Adam & Eve thread.

    fifthmonarchyman: The blooms might be grey but they are blooms they are not partial rocks.

    I guess they are related to grey squirrels either way.

  6. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: Again…………….
    I don’t deny common decent. I don’t reject the nested hierarchy.

    [snip]

    Although I don’t reject the nested hierarchy I do is reject the notion that the categorizations of human beings can be said to be objective.

    Again ….
    you try to create symmetry between the accepted scientific consensus and the speculations of creationist denialism. I thoroughly reject that.

  7. Allan Miller
    Ignored
    says:

    stcordova,

    Such precise repeat of a motif arising by chance point mutations on a pre-existing strand are very remote. At best maybe some sort of duplication, maybe tandem repeat, but then the problem arises of duplicating the zinc finger according to proper boundaries of the domain

    I think you need to show your working. Even randomly, there is a nonzero chance of a duplication happening between any given pair of bases. Having happened, its length will of course have a value, which means a nonzero chance of it having a particular right boundary too. Combined, is it really that miraculous? Miraculous, over the long run, would be the perpetual avoidance of a boundary.

    Three duplications are all that is needed to generate 8 repeats of the original sequence, with 7 apparently miraculous ‘internal’ boundaries if one naively imagines it happening one by one.

    Of course, it’s not random anyway. The very fact that a repeat has happened once makes it a target for misalignment during homologous base pairing. It’s mechanistic. Look up Copy Number Variation. Happens all the time; it’s a genealogical marker.

  8. fifthmonarchyman
    Ignored
    says:

    Corneel: About the big picture, but not about individual facts.

    Actually I was talking about certainty in relationships at that time as apposed to facts. Now it seems we are talking about the concept of certainty,

    To be honest the whole idea of certainty is boring to me. I would not ever bring up the topic here myself. It’s like talking about a persons sense of humor or how pleasant he is.

    It simply describes the confidence a person has in this or that thing. As such it is by definition a subjective thing individual to that person. As such it’s very different than objectivity.

    I’ve known lots of folks who are mistakenly certain and wrong at the same time all the time.

    In fact I have a tendency be certain more often than I’d like. It’s just an individual proclivity of mine.

    A person’s certainty or lack of it tells you nothing about anything outside his own mind.

    Corneel: If we acknowledge that every observation of the world, no matter how mundane, is tainted by subjective bias, then we must also concede that complete certainty is unattainable.

    You apparently mean something by certain that I don’t.

    I can be certain that I love my pizza. That would simply be an expression of the confidence I have in my own biased opinion.

    Subjectivity and certainty are not antonyms. They are not even terribly related terms

    Corneel: And you have been using that argument to dismiss unwelcome facts that happen to be backed up by mainstream science

    I’m not dismissing anything.

    All I’m doing is placing “science” in it’s proper place. Too often folks here treat science like it’s something it was never intended to be. A scientific finding is never the final word on anything.

    It’s always simply the best conclusion we have with the information available to us now. To treat it as more than that is to go beyond what is warranted

    I don’t think any scientist would argue with that characterization

    Corneel: I guess they are related to grey squirrels either way.

    Grey blooms are the same color as grey squirrels so they are related in that way. Only a Darwinist would assume that similarity automatically equals genetic kinship.

    Corneel: you try to create symmetry between the accepted scientific consensus and the speculations of creationist denialism. I thoroughly reject that.

    That’s OK we all have opinions about things
    I like grape juice.

    I’m not arguing that your chosen theory and YEC are equally supported by the evidence or equally likely to be true or anything like that.

    I’m only pointing out the obvious truth that your chosen theory is not objective reality. It can’t be.

    Because of, you know —logic

    peace

  9. OMagain
    Ignored
    says:

    FMM rejects the notion that objective categorization is possible. The world shrugs it’s shoulders.

    So what? they cry. It’s not like FMM is in a position where his opinion counts for squat.

  10. OMagain
    Ignored
    says:

    Allan Miller: I think you need to show your working.

    I’d actually be more interested in Sal explaining how Intelligent Design solves this problem rather then hearing a mangled misunderstood version of what Sal has misinterpreted.

  11. Entropy Entropy
    Ignored
    says:

    Allan Miller: … if one naively imagines it happening one by one …

    Sal thinks that if it doesn’t happen one by one (point mutations), then it’s not evolution. Not only that, if it’s not point mutations, then it’s magic (god-did-it), even if scientists have observed the natural phenomena involved.

    ETA: I think it goes like this in Salvador’s mind:
    not point mutations -> not evolution -> not evolution -> god did it.

  12. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: I’ve known lots of folks who are mistakenly certain and wrong at the same time all the time.

    Will you believe it? I’ve met one online recently as well.

    fifthmonarchyman: I can be certain that I love my pizza. That would simply be an expression of the confidence I have in my own biased opinion.

    That doesn’t work for me. Going by your definition, in what sense is the observation “I love my pizza” biased? Are your feelings about your food preferences distorted? Do you think you’ve let your prejudices about italian food cloud your taste sensation? If so, then how can you be 100% certain that you love your pizza? If not, then how is this not a dry objective fact about your food preference?

    Now if you were to say: “Pizza tastes great”, I would agree that that would clearly be a subjective statement.

    fifthmonarchyman: It’s always simply the best conclusion we have with the information available to us now. To treat it as more than that is to go beyond what is warranted

    I am not asking for more. I am asking for exactly that: to treat it as the best conclusion we have with the information available to us now. Like HERE:

    fifthmonarchyman: Only a Darwinist would assume that similarity automatically equals genetic kinship.

    No, a “Darwinist” would not do that. You are simply resisting the -in your own words- best conclusion we have with the information available to us now.

    fifthmonarchyman: I’m not arguing that your chosen theory and YEC are equally supported by the evidence or equally likely to be true or anything like that.

    I’m only pointing out the obvious truth that your chosen theory is not objective reality. It can’t be.

    Because of, you know —logic

    No, you are not “merely pointing things out”. You were disputing that an objective nested hierarchy could be discovered by humans. Worse, you maintained that everybody imposes some distoring worldview bias on the things that we observe in the world. To me, that sounds like you are trying to rationalize away inconvenient facts from mainstream science that conflict with your worldview.

  13. fifthmonarchyman
    Ignored
    says:

    Corneel: That doesn’t work for me. Going by your definition, in what sense is the observation “I love my pizza” biased? Are your feelings about your food preferences distorted?

    Bias is not a derogatory term in this context. It simply means that my feelings are mine and not universal. Someone else’s experience of food preference would be different than mine. How I understand “like” and “pizza” and “I” is not exactly the same as someone else would.

    Corneel: If so, then how can you be 100% certain that you love your pizza?

    All that is required is that I have total confidence that I love pizza. It might very well be a foolish confidence. It makes no difference

    My “certainty” is not a measure of the reality of the situation it’s only a measure of my confidence.

    Corneel: Now if you were to say: “Pizza tastes great”, I would agree that that would clearly be a subjective statement.

    Actually it’s only when you include the implied “to me” that the statement is clearly subjective.

    Corneel: You are simply resisting the -in your own words- best conclusion we have with the information available to us now.

    You need to speak for your self

    I might very well have more or better information than you do.

    Corneel: You were disputing that an objective nested hierarchy could be discovered by humans.

    Yes that is because humans are subjective and therefore any categorization they do will inevitably have subjective elements.

    There is no avoiding this unless you are God

    Corneel: Worse, you maintained that everybody imposes some distoring worldview bias on the things that we observe in the world.

    Of course we all do. It’s called a worldview because it’s the way we view the world after all.

    Unless you can demonstrate that your worldview is different from everyone else’s in that it’s uniquely objective it’s inevitable that there will be differences between what you observe and objective reality. It’s what it means to be human.

    Corneel: To me, that sounds like you are trying to rationalize away inconvenient facts from mainstream science that conflict with your worldview.

    I have no idea what “inconvenient facts” you are referring to.

    I know of no facts that conflict with my worldview from “mainstream science” or otherwise.

    If you have evidence that I am rationalizing away facts I would appreciate you share it with me.

    Incidentally when you say things like “To me, that sounds like” you are making your own inherent subjectivity explicit.

    I only wish folks from your side would preface more of their subjective opinions like that.

    It would certainly make the world a more peaceful place 😉

    peace

  14. PeterP
    Ignored
    says:

    hmm

    fifthmonarchyman: Not necessarily any difference at all. The point was that there is something between certain and dubious. Why do you ask?

    there is no difference at all between partially or somewhat certain. I asked because you presented it as if there was some discernible difference.

    hmmfifthmonarchyman: No when you can’t quantify something that means that terms like “equal” have no meaning.

    If you cannot quantify certainty then there is no difference whatsoever between any claims/opinions.

    fmmfifthmonarchyman: Saying that nighttime is the opposite of daytime does not mean that 8 PM and 1 AM are equal. It just means neither is daytime and they never can be daytime .

    Now that is some confused and twisted thinking you got going there. Around here there are times when the sun doesn’t set until 8:45 pm which means that 8 pm would qualify as daytime unless you hold to some very odd definition of daytime.

    There are also places on the Earth where at times the sun doesn’t set at all which would make both 1 am and 8 pm as being daytime. Don’t you ever grow weary of being so wrong on so many things?

    fifthmonarchyman: Does that mean that you agree that humans can’t be completely impartial or does it mean that you think it’s nonsense to say that humans can’t be completely impartial?

    the latter

  15. fifthmonarchyman
    Ignored
    says:

    Corneel: No, a “Darwinist” would not do that.

    Are you actually claiming that physical similarity is not considered to be evidence for kinship in Neo-Darwinism all things being equal?

    I would bet that would come as a surprise to most folks who hold to that school of thought.

    If physical similarity is not considered to be evidence for kinship why is the nested hierarchy so important?

    peace

  16. fifthmonarchyman
    Ignored
    says:

    PeterP: there is no difference at all between partially or somewhat certain.

    Whether there is or not is irrelevant to my point.

    PeterP: I asked because you presented it as if there was some discernible difference.

    That is your subjective opinion.

    I was only pointing out that unlike the binary objective-subjective paring of antonyms certain-dubious is an attitude continuum for which it is possible have feelings somewhere in the middle or closer to one extreme or the other.

    PeterP: Around here there are times when the sun doesn’t set until 8:45 pm which means that 8 pm would qualify as daytime unless you hold to some very odd definition of daytime.

    You are making my point for me.

    That is exactly why all human categorizations are subjective.

    For me anytime after dinner is nighttime. This is probably because I get up very very early.

    Your mileage will vary. You are after all human with your own subjective perspective.

    PeterP: There are also places on the Earth where at times the sun doesn’t set at all which would make both 1 am and 8 pm as being daytime.

    How can someone prove my point about subjectivity and at the very same time think it proves that I’m wrong?

    Such is the power of worldview.

    PeterP: the latter

    You actually think that you could would weigh every possible opinion equally in every conceivable choice you make.

    That is a mighty high opinion of yourself you have there.

    Are you sure you have given the same exact same intellectual consideration to folks who think it’s possible you might occasionally be mistaken?

    Peace

    peace

  17. PeterP
    Ignored
    says:

    fmm

    fifthmonarchyman: For me anytime after dinner is nighttime. This is probably because I get up very very early.

    What does getting up early and dinnertime have to do with the concept of ‘daytime’ and ‘nighttime’ outside of your own personal definition of the two? Do you think that when you close your eyes it is ‘nighttime’?

    fifthmonarchyman: You actually think that you could would weigh every possible opinion equally in every conceivable choice you make.

    the need to resort to a straw man characterization of the topic demonstrates your desperation. Here is the topic:

    PeterP: fifthmonarchyman: Does that mean that you agree that humans can’t be completely impartial or does it mean that you think it’s nonsense to say that humans can’t be completely impartial?

    Nowhere did you say: ” could would weigh every possible opinion equally”. I also don’t think it is an opinion that there are places on Earth where the sun does not set at certain times of the year that is an objective fact. Do you think that the Sun not setting at some points on Earth at some points in time represents a subjective opinion? Or is it reasonable to conclude that no one observing the Sun at these locations and times would ever see the Sun set? I realize that asking that question of someone who believes that getting up early and going to bed after dinner somehow defines ‘daytime’ and nighttime’ is a futile endeavor but your responses are just so funny it is hard to resist.

    fifthmonarchyman: PeterP: There are also places on the Earth where at times the sun doesn’t set at all which would make both 1 am and 8 pm as being daytime.

    How can someone prove my point about subjectivity and at the very same time think it proves that I’m wrong?

    thems are just the facts unlike your idiosyncratic usage of ‘daytime’ and ‘nighttime’. Nothing subjective at all and I would state that what I presented are objective facts.

  18. fifthmonarchyman
    Ignored
    says:

    PeterP: Do you think that when you close your eyes it is ‘nighttime’?

    I think that daytime is when daytime activities are supposed to happen and nighttime is when nighttime activities are supposed to happen. It’s roughly bounded by sunset and sunrise

    Do you think daytime and nighttime is determined by an official clock in Greenwich England or something?

    It’s funny how your whole line of questioning is proving my point here.

    These things are binary and our perspectives are inherently subjective.

    PeterP: Nowhere did you say: ” could would weigh every possible opinion equally”.

    Do you even understand what it means to be objective?? It requires you to do that by definition. You can’t be biased or partial in anyway. You can’t regard the opinion of a trusted friend or leaned scientist to be worth more than that of the village idiot.

    That is just one obvious reason why you as a human can’t be completely objective.

    PeterP: Do you think that the Sun not setting at some points on Earth at some points in time represents a subjective opinion?

    1) The experience of time is relativistic. your position in space matters
    2) Determining when the sun sets in a particular place is subjective. The times given by weather services assume a abstractly smooth surface.
    They don’t include things like mountains or trees or buildings that will effect our experience of sunset or sunrise.

    3) sunrise and sunset are not the official boundaries of daytime and nighttime.
    For instance sunrise tomorrow is at 7:02 AM and sunset is at 7:26 PM no one thinks that 7:01 AM is nighttime and 7:25 PM is daytime.

    We simply don’t think like that. We aren’t machines

    PeterP: thems are just the facts unlike your idiosyncratic usage of ‘daytime’ and ‘nighttime’.

    How exactly do you demonstrate that your understanding exactly reflects objective reality while that of everyone else does not?

    Hint: Claiming something is a fact does not constitute a demonstration.

    peace

  19. PeterP
    Ignored
    says:

    fmm

    fifthmonarchyman: I think that daytime is when daytime activities are supposed to happen and nighttime is when nighttime activities are supposed to happen. It’s roughly bounded by sunset and sunrise

    What constitutes ‘daytime’ activities and ‘nighttime’ activities?

    fifthmonarchyman: Do you think daytime and nighttime is determined by an official clock in Greenwich England or something?

    Not at all.

    fifthmonarchyman: Do you even understand what it means to be objective?? It requires you to do that by definition. You can’t be biased or partial in anyway. You can’t regard the opinion of a trusted friend or leaned scientist to be worth more than that of the village idiot.

    I certainly understand what objective means but it doesn’t appear that you have a grasp of the concept.

    Yes, I agree testimonials from religious folks regarding their experiences are of no more value than someone who claims their use of a Hulda Clark zapper cured them of cancer.

    fifthmonarchyman: PeterP: Do you think that the Sun not setting at some points on Earth at some points in time represents a subjective opinion?

    1) The experience of time is relativistic. your position in space matters
    2) Determining when the sun sets in a particular place is subjective. The times given by weather services assume a abstractly smooth surface.
    They don’t include things like mountains or trees or buildings that will effect our experience of sunset or sunrise.

    Of course I didn’t ask you about determining when the sun sets in a particular place. Your like a student who doesn’t know the answer to the question posed so they make up their own question to answer.

    fifthmonarchyman: 3) sunrise and sunset are not the official boundaries of daytime and nighttime.
    For instance sunrise tomorrow is at 7:02 AM and sunset is at 7:26 PM no one thinks that 7:01 AM is nighttime and 7:25 PM is daytime.

    Of course not since getting up early and going to bed after dinner are the boundaries according to you. Or is it when daytime and nighttime (whatever they are) activities are supposed to happen?

    fifthmonarchyman: How exactly do you demonstrate that your understanding exactly reflects objective reality while that of everyone else does not?

    Hint: Claiming something is a fact does not constitute a demonstration.

    I provided the scenario to test the objectivity of the sun not setting. You studiously avoided addressing that scenario and are now trying to pretend it was never presented. Grade school kids have done the experiment in countless classrooms around the world. Maybe you were absent that day?

  20. fifthmonarchyman
    Ignored
    says:

    PeterP: What constitutes ‘daytime’ activities and ‘nighttime’ activities?

    Again it depends on who you are. If you work the night shift daytime activities include sleep and nighttime activities include work.

    All of this is very subjective and personal.

    PeterP: Yes, I agree testimonials from religious folks regarding their experiences are of no more value than someone who claims their use of a Hulda Clark zapper cured them of cancer.

    As much as you would like to make it so this is not about religion.

    It’s about partiality and finite perspective because you have those things it’s logically impossible for you to be completely objective.

    It’s a part of being human

    PeterP: Of course I didn’t ask you about determining when the sun sets in a particular place.

    but if we agree that the time of sunset is important when we discuss what counts as daytime and nighttime. Then the time sunsets is also important. Don’t you agree.

    PeterP: Your like a student who doesn’t know the answer to the question posed so they make up their own question to answer.

    This is not a lecture but a discussion.

    If you ask me a silly irrelevant question meant to score empty points with the peanut gallery don’t expect me to feel obligated to answer it in a way that only compounds the silliness.

    PeterP: Of course not since getting up early and going to bed after dinner are the boundaries according to you.

    How did you possibly come to that conclusion??

    In the the very last comment I said the boundaries are roughly sunset and sunrise.

    Are you being deliberately obtuse and combative?

    PeterP: Or is it when daytime and nighttime (whatever they are) activities are supposed to happen?

    Why are you having difficultly here. Is it because you still want to be able to measure the distance of a particular time from the boundary for some reason?

    As I said before it does not work like that. It’s binary.

    8:00 pm is not less nighttime or more daytime than 1:am. They are both nighttime.

    PeterP: I provided the scenario to test the objectivity of the sun not setting.

    Are you kidding me?? You actually think the setting of the sun is objective??

    If I’m interstellar space traveling at the speed of light what time exactly does the sun set for me and nighttime begin??

    LOL

    PeterP: Grade school kids have done the experiment in countless classrooms around the world. Maybe you were absent that day?

    Do you actually think that grade school kids “discover” the objective time that the sunrises rather than an approximation based on an abstraction?

    Here is how it is calculated

    quote:
    For precision`s sake, the times are calculated as the moments when the geocentrical center of the sun is 50 minutes of arc below the horizon–34 minutes as a set value for refraction plus 16 minutes for the semidiameter.
    end quote:

    from here
    http://www.chicagotribune.com/news/ct-xpm-1985-07-14-8502150709-story.html

    Does that sound like something that humans can ever experience objectively? really?

    peace

  21. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    Looks to me like yet another conversation that has run aground because of a failure to distinguish the objective/subjective and absolute/relative distinctions.

  22. dazz dazz
    Ignored
    says:

    fifthmonarchyman: I think that daytime is when daytime activities are supposed to happen and nighttime is when nighttime activities are supposed to happen

    true genius

  23. Entropy Entropy
    Ignored
    says:

    Kantian Naturalist:
    Looks to me like yet another conversation that has run aground because of a failure to distinguish the objective/subjective and absolute/relative distinctions.

    That’s because the ability to distinguish distinctions is distinctively absent among presuppositionalists.

  24. fifthmonarchyman
    Ignored
    says:

    Kantian Naturalist: Looks to me like yet another conversation that has run aground because of a failure to distinguish the objective/subjective and absolute/relative distinctions.

    That is my impression as well.

    It seems that lots of folks here think that there are no clear distinctions between these concepts.

    They seem to believe that something can be part objective and part subjective or part absolute and part relative.

    These folks need to refresh their understanding of the law of the excluded middle.

    peace

  25. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman,

    I will leave the objective-subjective discussion for what it is, because when you argued that you were very confident that you liked pizza, but that this was no measure of the reality of this situation, I frankly gave up.

    Instead, I’d like to react to this:

    fifthmonarchyman: Are you actually claiming that physical similarity is not considered to be evidence for kinship in Neo-Darwinism all things being equal?

    I would bet that would come as a surprise to most folks who hold to that school of thought.

    If physical similarity is not considered to be evidence for kinship why is the nested hierarchy so important?

    Indeed, a phylogenetic tree is not built on mere similarity, but on the distribution of shared uniquely derived characters (synapomorphies). This does not come as a surprise to “folks who hold to that school of thought”, but must have been explained a dozen times before here on this site by John, Joe and others.

    Mere physical similarity is not considered sufficient evidence for kinship, because certain characters are known to be unreliable for clustering related groups, for example because they are known to rapidly evolve (*cough*fur colour*coughcough*).

  26. fifthmonarchyman
    Ignored
    says:

    Corneel: Indeed, a phylogenetic tree is not built on mere similarity, but on the distribution of shared uniquely derived characters (synapomorphies).

    I never said otherwise.
    My point was that according to Neo-Darwinism similarity is evidence for common decent. I never claimed it was the only evidence.

    I also never claimed that the nested hierarchy was built “merely” on similarity.

    Instead I said that the nested hierarchy is supposed to be an important argument for common decent because physical similarity is considered to be evidence for kinship.

    I’m afraid you are setting up a straw man. Instead of actually interacting with what is being said.

    Corneel: Mere physical similarity is not considered sufficient evidence for kinship

    I also never said physical similarity was sufficient evidence for kinship. Again I’m not sure who you are countering with your statement but it’s surely not me.

    Corneel: certain characters are known to be unreliable for clustering related groups, for example because they are known to rapidly evolve

    Now we are on to something.

    So you are saying that when it comes to the nested hierarchy criteria for groupings is often weighted according to a predetermined schema that will hopefully yield a sought after result.

    My point exactly!!!!!!!!!!!
    Glad we are in agreement.

    That is what Ive been saying all along while John and others have been adamant that uniquely in the case of nested hierarchy we let the data lead us instead of the other way around.

    Corneel: for example because they are known to rapidly evolve.

    So our best evidence for common decent is a grouping that has been deliberately set up so as to minimize characteristics that we might expect would come from things other than common decent.

    Can you see why that might be a problem??

    Can you see why it might be considered a stretch to call the resulting grouping “objective”??

    peace

  27. Corneel Corneel
    Ignored
    says:

    Let’s first tackle this:

    fifthmonarchyman: Instead I said that the nested hierarchy is supposed to be an important argument for common decent because physical similarity is considered to be evidence for kinship.

    I’m afraid you are setting up a straw man. Instead of actually interacting with what is being said.

    No, you said that only a Darwinist would assume that similarity automatically equals genetic kinship, which is clearly false. You seem to be in the habit of forgetting what it was you actually claimed and blaming other people when you are called out on it. Perhaps you could stop that?

    fifthmonarchyman: I also never said physical similarity was sufficient evidence for kinship. Again I’m not sure who you are countering with your statement but it’s surely not me.

    As above, I reacted to your claim that a Darwinist would automatically take that as sufficient evidence for kinship. You definitely did say that.

  28. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: So you are saying that when it comes to the nested hierarchy criteria for groupings is often weighted according to a predetermined schema that will hopefully yield a sought after result.

    [..]

    That is what Ive been saying all along while John and others have been adamant that uniquely in the case of nested hierarchy we let the data lead us instead of the other way around.

    Hoo boy.

    No, that is not what John cum suis have been saying. He claimed that there exists an objective nested hierarchy that we can discover through investigation (which is correct). You have been denying this by constructing some ridiculous artificial classification scheme in which grey squirrels grouped with grey wolves, and arguing that this scheme is of equal value because both are “subjective” (which is utter nonsense).

    The reason why the phylogenetic classification is more likely to reflect the objective nested hierarchy is exactly because systematists observe certain standards for picking suitable characters, rather than cherry-picking characters that support a preferred pre-determined scheme, like you did. Please also note that they pick characters without regard for any specific branching order.

    fifthmonarchyman: So our best evidence for common decent is a grouping that has been deliberately set up so as to minimize characteristics that we might expect would come from things other than common decent.

    Can you see why that might be a problem??

    You know. I have this crazy thing. If I want to learn something about, say, beetles, I actually look up books about beetles. I try to minimize the number of books about Polish folk dancing or knitting lamp shades. So how exactly is it a problem to look at characteristics that are relevant for the thing you are interested in?

    fifthmonarchyman: Can you see why that might be a problem??

    Can you not see that looking at relevant characters does not guarantee that you find a phylogenetic tree? You can only find it if there really is some underlying genealogical history (or a deceptive Designer).

  29. fifthmonarchyman
    Ignored
    says:

    Corneel: No, you said that only a Darwinist would assume that similarity automatically equals genetic kinship, which is clearly false.

    That was a joke.

    We were discussing a relationship between a grey rock and a grey flower. Clearly it’s absurd that such a relationship implies kinship. That is what makes it funny

    I expected you of all people to understand the humor.

    Corneel: As above, I reacted to your claim that a Darwinist would automatically take that as sufficient evidence for kinship.

    Come on man relax. Surely you chuckled at the thought of a rock and a flower sharing a common ancestor?

    If you can’t have a little fun once and a while these discussions will get to you.

    peace

  30. fifthmonarchyman
    Ignored
    says:

    Corneel: You have been denying this by constructing some ridiculous artificial classification scheme in which grey squirrels grouped with grey wolves, and arguing that this scheme is of equal value because both are “subjective” (which is utter nonsense).

    I never once said that my classification is of equal value. The value of a classification scheme depends on it’s usefulness.

    My classification scheme draws attention to the interesting behavior of Grey foxes and the particular phenotypical constraints present in a forest habitat in that context it’s more valuable than yours.

    On the other hand your classification is more valuable when it comes to things like predicting genetic similarity between species.

    Again this is all about perspective. Classification systems are tools and the usefulness of a tool will vary depending on it’s intended use.

    Corneel: The reason why the phylogenetic classification is more likely to reflect the objective nested hierarchy is exactly because systematists observe certain standards for picking suitable characters, rather than cherry-picking characters that support a preferred pre-determined scheme, like you did.

    Who exactly comes up with the “standards” that they use??

    Think hard about this one.

    Corneel: If I want to learn something about, say, beetles, I actually look up books about beetles.

    I do that as well and I also go out and look at some beetles. Sometimes I trust my own eyes more than the books. It depends on what my purpose was for learning about them in the first place.

    It’s all about perspective

    Corneel: Can you not see that looking at relevant characters does not guarantee that you find a phylogenetic tree?

    How exactly do you determine what characters are relevant. Does that determination influence the final product in any way?

    Can you see why that could be a problem?

    peace

  31. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: That was a joke.

    We were discussing a relationship between a grey rock and a grey flower. Clearly it’s absurd that such a relationship implies kinship. That is what makes it funny

    I expected you of all people to understand the humor.

    [..]

    Come on man relax. Surely you chuckled at the thought of a rock and a flower sharing a common ancestor?

    If you can’t have a little fun once and a while these discussions will get to you.

    Ok, I definitely missed that one. In my defense; your sincere statements and your jokes are becoming a bit hard to separate in this thread.

    Anyway, subtleties may sometimes be lost in online conversations, and I apologise if my comments came across a bit cranky.

  32. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: On the other hand your classification is more valuable when it comes to things like predicting genetic similarity between species.

    How about its value in describing the correct evolutionary relationships among lineages? Is “my” classification useful for that as well?

    fifthmonarchyman: Who exactly comes up with the “standards” that they use??

    Think hard about this one.

    Gnnnn! Ok, I would say these standards are developed by consensus within the field of systematics. Not OK?

    fifthmonarchyman: I do that as well and I also go out and look at some beetles. Sometimes I trust my own eyes more than the books. It depends on what my purpose was for learning about them in the first place.

    And doesn’t that sound reasonable? So why do you criticise systematists for looking at characters that are most likely to inform them about phylogenetic relationships?

    fifthmonarchyman: How exactly do you determine what characters are relevant. Does that determination influence the final product in any way?

    No it does not. This is the issue that you are confused about, so pay attention: To select characters that are most informative about phylogenetic relationships does not favor any particular phylogenetic tree. That is, this procedure does not push any preferrred classification, but it optimises the chance of detecting the correct evolutionary branching order, and along with that the objective nested hierarchy. By uncovering this particular tree, in multiple independent data sets, common descent is strongly supported.

  33. stcordova
    Ignored
    says:

    I appreciate all who’ve kept the discussion alive in my absence.

    There are two phylogenies, and not necessarily equal, the pFAM phylogeny and then whatever organismal phylogenies that are out there.

    I have next to zero experience with pFAM. Establishing promiscuous domains might be better done by looking at the pFAM phylogenies, and then seeing which domains were promiscuously appearing. Of course, if the protein has no ancestor, that is a major problem for common descent.

  34. Entropy Entropy
    Ignored
    says:

    stcordova:
    There are two phylogenies, and not necessarily equal, the pFAM phylogeny and then whatever organismal phylogenies that are out there.

    They should be different Sal. The domains are found in different proteins, so their histories should reflect their duplication/recombination events, besides their divergences with the organisms that carry them.

    stcordova:
    I have next to zero experience with pFAM.Establishing promiscuous domains might be better done by looking at the pFAM phylogenies, and then seeing which domains were promiscuously appearing.

    I have lots of experience with pFam and other domain databases. But that’s not needed to understand that it doesn’t make sense to build a phylogeny of a domain before establishing if the domain is promiscuous. They’re independent things, except in the sense that for promiscuous domains the phylogenetic reconstruction would be harder to produce (because of the abundance of sequences, too much computing to perform). There’s also the problem that if the domains are short and abundant, then they might not have enough informative positions for building a robust phylogeny. But, again, you don’t need the phylogeny to figure out if the domains are promiscuous.

    stcordova:
    Of course, if the protein has no ancestor, that is a major problem for common descent.

    You need to be more precise in your writing. Here it seems as if you’re saying that proteins should always have ancestors (ancestral proteins?), but new proteins arise from time to time. Those new proteins would have no ancestors (except in the form of prior DNA sequences that did not encode for proteins), and they do not falsify common ancestry. They’re just new proteins, and, eventually, will make new families. Those new families will trace their common ancestry to the, for now, new protein.

    So, maybe you meant something other than “the protein”?

  35. fifthmonarchyman
    Ignored
    says:

    Corneel: Anyway, subtleties may sometimes be lost in online conversations, and I apologise if my comments came across a bit cranky.

    No problem.

    I agree that subtleties are often lost when you can’t see each others face. There is also the problem of the huge communication gap that results from our starting from radically different worldviews.

    As a helpful guide keep in mind that I’m a just a lovable teddy bear and would never say anything intentionally to upset you for no reason.

    That is what I try and do when I question some of the things you might say off the cuff from time to time.

    Corneel: How about its value in describing the correct evolutionary relationships among lineages? Is “my” classification useful for that as well?

    I think you know that I would tentatively say yes it is. I have no problem with that conclusion pending new evidence of course.

    Corneel: I would say these standards are developed by consensus within the field of systematics. Not OK?

    No it’s OK.
    But it’s definitely not “discovery” or “objective”.

    The folks who make the groupings decide amongst themselves what is important and what is not. That is a perfectly acceptable but subjective way of doing things

    Corneel: So why do you criticise systematists for looking at characters that are most likely to inform them about phylogenetic relationships?

    I’m not criticizing systematists for anything. I’m criticizing internet popularizers who claim the results of the systematists labor is compelling evidence for common decent. It’s not

    Corneel: To select characters that are most informative about phylogenetic relationships does not favor any particular phylogenetic tree.

    I never claimed it did.

    I think you are confusing the general idea of common descent with a particular phylogenetic tree.

    As long as we choose to look at characters that we suppose are most likely to lead to discovering a familial relationship we will tend to find a familial relationship. It might not be the one we expect but it will be one none the less. (all things being equal).

    Corneel: this procedure does not push any preferrred classification, but it optimises the chance of detecting the correct evolutionary branching order

    Evolutionary branching order is a classification schema is it not??

    In fact it’s the
    “preferred classification” schema of systematists working on the nested hierachy.

    That is the point.

    Corneel: and along with that the objective nested hierarchy.

    Here is where you are going off the rails. I don’t think that anyone is arguing that the particular nested hierarchy we have right now is “The” objective one. That would be clearly false. Adjustments are made to our trees all the time sometimes radical adjustments.

    What they are arguing I believe is that the over all general linnaean system is uniquely objective. As apposed to some other classification system.

    That is the claim that I’m disputing.

    peace

  36. Mung Mung
    Ignored
    says:

    stcordova: Of course, if the protein has no ancestor, that is a major problem for common descent.

    Nothing is a problem for common descent. New proteins can appear de novo from the primordial DNA soup. In fact, we see this all the time. It’s why so many groups of organisms have so many different protein families that cannot be fit into an objective nested hierarchy.

  37. OMagain
    Ignored
    says:

    Mung: Nothing is a problem for common descent. New proteins can appear de novo from the primordial DNA soup. In fact, we see this all the time. It’s why so many groups of organisms have so many different protein families that cannot be fit into an objective nested hierarchy.

    Good caricature of Sal’s evolution strawman, yes.

  38. fifthmonarchyman
    Ignored
    says:

    Mung: It’s why so many groups of organisms have so many different protein families that cannot be fit into an objective nested hierarchy.

    It’s not a problem if lots of things don’t fit.

    That is because the things that do fit are more important. More important to who you ask?

    Why to the folks making the categorization of course.

    peace

  39. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: Corneel: To select characters that are most informative about phylogenetic relationships does not favor any particular phylogenetic tree.

    Fifth: I never claimed it did.

    I think you are confusing the general idea of common descent with a particular phylogenetic tree.

    Au contraire. It is you that confuses the general idea of common descent with a particular phylogenetic tree, and by doing so you implicitly make that claim. Here is the thing: you can’t force consilience of multiple independent trees without deciding beforehand what that particular tree should look like. If you don’t do that, you get a tree without any statistical support, which cannot be used as evidence for common descent.

    fifthmonarchyman: Evolutionary branching order is a classification schema is it not??

    The classification is based on the nodes of the evolutionary tree. The idea is to group organisms that are more closely related to each other than to any members outside the group.

    fifthmonarchyman: Here is where you are going off the rails. I don’t think that anyone is arguing that the particular nested hierarchy we have right now is “The” objective one. That would be clearly false. Adjustments are made to our trees all the time sometimes radical adjustments.

    Black-and-white thinking again. “Because it is not 100% correct, it is all wrong”. You just can’t help it, can you?

    fifthmonarchyman: What they are arguing I believe is that the over all general linnaean system is uniquely objective. As apposed to some other classification system.

    That is the claim that I’m disputing.

    You are mistaken: I agree that Linnean taxonomy is subjective, but we are talking phylogenetic systematics, which is based on evolutionary relationships. There can certainly be multiple equally valid classification systems, but there is only one tree that correctly reflects the evolutionary branching order.

  40. Allan Miller
    Ignored
    says:

    Mung: Nothing is a problem for common descent. New proteins can appear de novo from the primordial DNA soup. In fact, we see this all the time. It’s why so many groups of organisms have so many different protein families that cannot be fit into an objective nested hierarchy.

    Even after so many years, your woeful grasp of the subject matter is quite shocking.

  41. Corneel Corneel
    Ignored
    says:

    fifthmonarchyman: As a helpful guide keep in mind that I’m a just a lovable teddy bear

    Perhaps you need a new avatar?

  42. Rumraket Rumraket
    Ignored
    says:

    stcordova: Of course, if the protein has no ancestor, that is a major problem for common descent.

    No, that is a problem with inferring common descent using that protein.

    But common descent does not entail that all proteins must be able to be traced to a common ancestor, as common descent does not make claims about the rate at which (or even how) proteins are lost and gained. Even though in many cases we have good evidence of how that happened. Particularly at the resolution offered by more recent divergence times, as using comparative genetics we can basically see how the noncoding DNA in closely related species gradually evolve into de novo protein coding regions in particular species.

  43. stcordova
    Ignored
    says:

    No, that is a problem with inferring common descent using that protein.

    Well you can’t infer common descent with it. That’s exactly the point! It’s evidence against common descent. Same for every other poofomorphy with no ancestral form.

  44. Entropy Entropy
    Ignored
    says:

    stcordova:
    Well you can’t infer common descent with it.That’s exactly the point!

    Really? So the point is, exactly, that a new protein, which obviously cannot be used to infer common ancestry, cannot be used to infer common ancestry? I don’t understand why an obvious consequence of a protein being new would be an important point to make. It’s obvious.

    stcordova:
    It’s evidence against common descent.

    Sorry, but it isn’t. Common ancestry is about the relationship of two or more things, namely, that they share a common ancestor. There’s nothing in there prohibiting new proteins to arise. This looks awfully like a non-sequitur Sal. An obvious non-sequitur. I’d avoid that if I were you, but then again, you don’t care ridiculing yourself and your own intellect, as long as those who you want to convince remain unaware of the stupidity involved in your claim. So, carry on as you wish. It’s your beliefs that get ridiculed by your incompetence.

    stcordova:
    Same for every other poofomorphy with no ancestral form.

    I always find it funny when creationists, who think that everything was poofed into existence, try and make fun of science by projecting their own beliefs in a ridiculing fashion. Irony-meters are exploding all over the place.

    I’m starting to think that your aim is to ridicule your purported beliefs. Otherwise you’d be much more careful.

  45. Rumraket Rumraket
    Ignored
    says:

    stcordova: Well you can’t infer common descent with it. That’s exactly the point! It’s evidence against common descent.

    No. For fecks sake all you IDcreationists keep making this basic error in reasoning. Something that fails to corroborate a hypothesis is not automatically evidence against the hypothesis UNLESS the hypothesis says it SHOULD confirm the hypothesis.

    But common descent does not say that there should not be proteins arising independently in separate lineages. So their mere existence can’t be evidence against common descent.

    How can you keep failing at the level of basic logic?

    There are aspects of my physiology that cannot be used to infer the close genalogical relationship I have with my brother (there are genes I got from our father that he didn’t, and the other way around, and the same with genes from our mother). That doesn’t make those genes evidence AGAINST us being brothers. It just means our relationship cannot be inferred using those particular genes.

    THINK.

  46. Entropy Entropy
    Ignored
    says:

    Rumraket,

    That was beautifully explained.

  47. fifthmonarchyman
    Ignored
    says:

    Rumraket: omething that fails to corroborate a hypothesis is not automatically evidence against the hypothesis UNLESS the hypothesis says it SHOULD confirm the hypothesis.

    I get your point and it’s a very good one.

    How about a list of things that correspond to that condition?

    The reason I ask is that unless you have sizable list that can be readily tested it begins to look like your hypothesis is not science.

    I should not have to explain to ID critics that a hypothesis must be falsifiable in reality and not just hypothetically.

    Hint: Please don’t fall back on idea that “an objective nested hierarchy would confirm the hypothesis” unless you can explain how we demonstrate that a particular nested hierarchy is objective.

    peace

  48. fifthmonarchyman
    Ignored
    says:

    Corneel: Black-and-white thinking again. “Because it is not 100% correct, it is all wrong”. You just can’t help it, can you?

    That is not at all what I’m saying.
    What I’m saying is that if something is not 100% correct we can’t say it’s 100% correct.

    In order for a particular tree to be considered the objective truth it must be 100% correct. That is just basic logic. That does not mean that a 90% correct tree is not wonderful and useful it only means that it is not the objective truth.

    When it comes to logic I do tend to be pretty black and white in my thinking. Respect for logic demands that sort of thing

    Corneel: Here is the thing: you can’t force consilience of multiple independent trees without deciding beforehand what that particular tree should look like. If you don’t do that, you get a tree without any statistical support, which cannot be used as evidence for common descent.

    Could you elaborate here? I don’t think the goal should be to “force” consilience in a single particular tree. The goal should be look at characters and groupings independently and see if there is any underlying connection between them.

    It’s highly possible that there is no single objective tree that we can discover. That is not a bad thing. Different trees for different perspectives and different purposes is a good thing I would say, The more information the better.

    As far as one particular tree being evidence for common decent I just don’t think it does the trick.

    There are just too many ways to legitimately and usefully group organisms. To get a single tree you have to overlook all the others.

    Corneel: I agree that Linnean taxonomy is subjective, but we are talking phylogenetic systematics, which is based on evolutionary relationships.

    Don’t get the cart before the horse

    There is no way to infer “evolutionary relationships” unless you assume common decent. If I understand the argument, Linnean taxonomy is supposed to be the supporting evidence for that assumption. I don’t think it able to meet that burden on it’s own.

    Corneel: There can certainly be multiple equally valid classification systems, but there is only one tree that correctly reflects the evolutionary branching order.

    Again you have to start with the idea that there is an “evolutionary branching order” before you can say that a particular tree correctly reflects that order.

    That is the piece that seems to be missing here.
    At least with the discussion at this particular website

    peace

  49. Mung Mung
    Ignored
    says:

    Rumraket: That doesn’t make those genes evidence AGAINST us being brothers. It just means our relationship cannot be inferred using those particular genes.

    Are you able to say precisely which genes brothers SHOULD share?

  50. Mung Mung
    Ignored
    says:

    Allan Miller: Even after so many years, your woeful grasp of the subject matter is quite shocking.

    You wouldn’t believe the amount of effort it takes.

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