Phylogenetic Systematics

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Let’s have a serious discussion about phylogenetic systematics.

What are the assumptions, the methods, and the inferences that can be drawn from phylogenetic analysis.

For example, is there anything to the creationist claim that phylogenetic systematics assumes common ancestry and does it even matter?

I’ll be using a number of different references such as Molecular Evolution: A Phylogenetic Approach and Molecular Evolution and Phylogenetics.

This thread will not be password protected, but it will be protected by angels.

1,034 thoughts on “Phylogenetic Systematics”

  1. Mung: You read the article by Theobald when you were 12 and that’s what convinced you that universal common ancestry was true?

    The TO page indicates that the article made its first appearance in 1999. So keiths was born in 1987. And keiths retired in 2017. After only 30 years. Nice. I’m jealous.

    I’m thinking that the Theobald article on TO had absolutely nothing to do with why keiths decided to accept universal common ancestry.

    If keiths decided that universal common ancestry was true prior to the publication of the Theobald article why did he do so? I’m thinking ignorance, but I could be wrong.

  2. colewd:

    They [computers] do John, and not only a nested hierarchy but an objective one.

    And:

    The computer example shows a designer will [create an objective nested hierarchy].

    OMagain:

    Can you link to where that objective nested hierarchy was shown, specifically? I’m interested. Objective as in others will be able to discern it, right?

    colewd:

    Get kieths link to Theobald and read about objective nested hierarchies. A designed hierarchy is in the discussion. I think you can connect the dots.

    No, Bill. OMagain is asking you to point to the computer example that shows that a designer will create an objective nested hierarchy. The one that you mentioned.

    It’s your claim. Can you support it, or will you fail again?

  3. Mung: Some say the inference to common ancestry from the nested hierarchy is independent of any causal process. Others say it is dependent upon a causal process. You seem to be in the latter camp.

    Is the causal process relevant or is it not?

    Depends on which causal process. What Allan is talking about is the causal process of biological inheritance. Without biological inheritance, no common descent; that’s what descent means.

    Don’t confuse that with the causal processes that result in the origin and fixation of innovation. That’s Sal’s job.

  4. keiths: It’s your ability that determines whether you can understand this stuff

    our ability as judged by keiths (or keiths authority) I guess.

    keiths: Anyone who thinks that this is a nested hierarchy, much less an objective nested hierarchy, is clueless:

    Instead of constantly complaining that your critics just don’t understand you another approach would be to explain the difference between the trees I presented and the three of life that purportedly entails common descent.

    That would certainly help to explain your position IMO.

    Zac had a problem with an element fitting into more than one nest but the tree of life has the same property.

    You claimed that your tree is “objective” while mine is subjective but you have yet to support that claim.

    Do you have anything else?

    peace

  5. our ability as judged by keiths (or keiths authority) I guess.

    No, fifth. It depends on your ability (or lack thereof), not on my assessment. This should be obvious.

    The ability is there (or in your case, not there) independent of my assessment of it.

    Even if no one had pointed it out or assessed your (in)ability, your mischaracterization of the quadrilateral hierarchy would still be a mistake.

    This is not difficult.

  6. keiths: This is not difficult.

    You became convinced of the truth of universal common ancestry after reading Theobald’s article? Or Theoblald’s article appeared long after you had already made up your mind.

    ETA: When did you first become convinced of the truth of universal common ancestry and when did you first read Theobald’s TO article?

  7. fifth,

    Why the Munglike helplessness? If you want to understand what makes a nested hierarchy a nested hierarchy, why not read about it? If you want to understand what makes a nested hierarchy objective, why not read about it?

    Again, this is not esoteric knowledge available only to initiates. It’s yours for the taking, but you have to make an effort.

  9. Mung: It doesn’t, necessarily. But I collect books, I like reading books, and I am far more likely to read a book and take it seriously.

    Yeah, my point is, I doubt one could really get a book out of it. I’d struggle to flesh the above out in an interesting way for the general reader (although better authors are of course available!). Dawkins’s Ancestors Tale is a pretty fair stab, following our lineage backwards and finding much of interest on the way. It’s not so much about the ‘evidence’ though; the reason we think there is a continuous lineage, and it’s not really about nodes and pairwise comparison at all. Though branching does come up.

    If no good arguments for universal common descent can be found in books then why can’t people just say so? If people were not convinced of the truth of universal common descent from reading a book why can’t they just say so?

    Well, I wasn’t, which is why I can’t think of one. Doesn’t mean there isn’t one, I’m just not aware and doubt it is bookworthy.

    My own story (again): as a pre-teen I was interested in the Linnaean hierarchy, being a keen bird watcher. A free poster in a magazine ended up on my wall, and it made perfect sense of the relationships – though just the animals. Learning molecular biology at uni turned it inside out; showed the genetic process that underlies the whole thing, which informs my sketch above. The digital nature of the process provides powerful confirmation of a view that was already well established on morphology alone, pre-1950’s.

    And it does appear that the commonalities go all the way to the roots: a single LUCA (not the first cell, before anyone starts).

  10. Mung,

    Some say the inference to common ancestry from the nested hierarchy is independent of any causal process. Others say it is dependent upon a causal process. You seem to be in the latter camp.

    No, it’s independent of any particular causal process, although obviously not all causal processes will lead to it. Anything that has a degree of copying fidelity, or inheritance, would be expected to lead to a hierarchy, as changes occurring at a particular point in the series of replications are inherited by all descendants, and a set can be formed of all possessors, nested within the greater set on other character states coalescing at other nodes.

    Template directed nucleic acid replication just happens to be the process underlying biology, not the only thing that would produce common descent and a nested hierarchy.

    It’s amazing to me that we have still not even agreed on this point. Who is right? Erik has been trying to explain this for months, and the best that keiths can do is ignore Erik’s point and erect a straw-man in its place.

    I find Erik weird, frankly. He does not seem able to articulate his point successfully, for all his hauteur, so I don’t really know what it is. He seems to be of the deny-at-all-costs persuasion.

  11. fifthmonarchyman: The letters on my computer keyboard are arranged in a QWERTY pattern not because the designer had to do it that way or because he was constrained by some sort of “ancestor-descendant relationship” but because it’s familiar to me and therefore I didn’t have to learn an entirely new pattern in order use it.

    Shows what you know.

  12. keiths: No, Bill. OMagain is asking you to point to the computer example that shows that a designer will create an objective nested hierarchy. The one that you mentioned.

    Yes, it’s quite clear. The claim is there is a “computer example” where an objective nested hierarchy can be demonstrated to exist in the relationships.

    colewd can either withdraw this claim as unsupported or acknowledge that he is without honor. It’s up to him.

  13. Mung:
    keiths cannot defend his beliefs and misrepresents the beliefs of others.

    Why, because he refuses to engage with your pointless questions?

    It’s clear who among us refuses to defend their beliefs and misrepresents the beliefs of others, quote miner extraordinaire Mung.

  15. fifthmonarchyman:
    God’s beliefs are not subjective. He is by definition objective.

    According to your “worldview,” meaning that according to your subjective opinion, this imaginary being’s subjective beliefs are objective “by definition.”

    Meh!
    😉

  16. fifthmonarchyman: Instead of constantly complaining that your critics just don’t understand you another approach would be to explain the difference between the trees I presented and the three of life that purportedly entails common descent.

    That would certainly help to explain your position IMO.

    Well, fifth, we have done that on multiple occasions, but you seem impervious.

    Zac had a problem with an element fitting into more than one nest but the tree of life has the same property.

    Actually, it doesn’t.
    Just because you can choose an attribute that does not nest (omnivory, color, size), that doesn’t mean that membership fails to nest.
    In response to my question:

    Is a square a rhombus, or is a square a rectangle?
    Because it cannot be both

    You replied

    I’d say a a square is a rhombus and a rectangle

    Just like a crow is a bird and an omnivore.

    Total fail. The analogous statement would be
    “Just like a crow is a bird and a mammal”
    Can you see the difference?
    I pointed out your attribute/member confusion when I originally asked the question.

  17. fifthmonarchyman:
    The letters on my computer keyboard are arranged in a QWERTY pattern not because the designer had to do it that way or because he was constrained by some sort of “ancestor-descendant relationship” but because it’s familiar to me and therefore I didn’t have to learn an entirely new pattern in order use it.

    The same goes for organisms on earth

    A lung of a mouse is pretty similar to the lung of an elephant or the lung of a human so you don’t have to start from scratch to understand the workings of each and every animal you encounter.

    That is a great gift and the hallmark of good design

    peace

    All organisms are composits of components, like atoms, photons, etc., so it doesn’t matter whether a lung of a mouse is similar to a stone or an elephant. Both are “good designs”, because you don’t have to start from scratch.

    However, isn’t “good design” measured by the requirements it has to fulfill? If the requirements contain “you have to understand by starting from scratch”, then similarities between components would constitute “bad design”.

  18. keiths:

    Now envision a process of common design, in which new design variations can be shared freely without any regard for ancestor-descendant relationships.

    fifth:

    What sort of designer would create like that? Certainly not a good one in my opinion.

    It shows no respect for continuity or flow and and makes comprehension of the design process difficult to impossible for observers.

    You’re making a silly logic mistake. The removal of a constraint does not compel a designer to adopt any particular style of design. It simply means he can operate without being bound by that constraint.

    And one can easily show respect for conventions, such as the QWERTY keyboard layout, without being bound by ancestor-descendant relationships.

    Why not do the exercise I suggested so that you can gain an understanding of the constraint we’re discussing?

    Just think about it. Use pencil and paper, if necessary. Start with an ancestral organism and assign a stylized genetic sequence to it. Simulate a process of common descent in which ancestral sequences are passed from parent to offspring with occasional copying errors. As new variants arise, place them in a tree in a way that represents the genealogical relationships. Label each node with the modified genetic sequence it possesses.

    Note the distinctive pattern that emerges, in which a variation, once it arises, is passed down from the ancestor in which it appears to that ancestor’s own descendants, rather than getting scattered arbitrarily all over the tree.

    Note that this distinctive pattern is reinforced as more and more variations arise and are passed down from ancestors to their own descendants. The new variations fit into the same pattern.

    Now envision a process of common design, in which new design variations can be shared freely without any regard for ancestor-descendant relationships. Without that limitation, the distinctive pattern associated with common descent no longer arises.

    Keep playing around with this, on paper, until the signficance and distinctiveness of the common descent pattern becomes obvious to you.

    I know your impulse is to disagree without understanding, but try to suppress that urge and approach this rationally, instead.

  19. DNA_Jock: Total fail. The analogous statement would be
    “Just like a crow is a bird and a mammal”
    Can you see the difference?
    I pointed out your attribute/member confusion when I originally asked the question.

    it’s not confusion

    The “nest” we put crows into depends on the attribute we are focusing on. If we are looking at the feathers attribute they are placed in the birds nest if we are looking at diet the fit into the “omnivores” nest, if we are looking at walking legs they fit into the “bipedal” nest.

    But even granting your point for the sake of argument what “nest” does lichen fit into? What about the Beefalo? the Lonicera fly? the Mariana mallard? The Red wolf?

    More fundamentally since presumably eukaryotes arose from a merger of Proteobacteria and Archaeans what ancestral nest do we fit in?

    peace

  20. PopoHummel: All organisms are composits of components, like atoms, photons, etc., so it doesn’t matter whether a lung of a mouse is similar to a stone or an elephant. Both are “good designs”, because you don’t have to start from scratch.

    Are you saying an observer could understand a “stone lung” as quickly and easily as one that is similar to those he had already encountered?

    PopoHummel: If the requirements contain “you have to understand by starting from scratch”, then similarities between components would constitute “bad design”.

    Yes, I would suppose that if the design requirement is that the world be borderline incomprehensible to us then we would not expect a nested hierarchy.
    or any discernible pattern at all for that matter.

    Since our ability to understand the world is not at all a concern of darwininistic evolution it’s very lucky that things turned out they way they did. 😉

    peace

  21. DNA_Jock:

    Just because you can choose an attribute that does not nest (omnivory, color, size), that doesn’t mean that membership fails to nest.

    fifth:

    it’s not confusion

    The “nest” we put crows into depends on the attribute we are focusing on. If we are looking at the feathers attribute they are placed in the birds nest if we are looking at diet the fit into the “omnivores” nest, if we are looking at walking legs they fit into the “bipedal” nest.

    You just demonstrated that it is confusion and that DNA_Jock’s diagnosis is correct.

  22. stcordova: You didn’t answer my question.

    That’s funny. We introduced a question concerning the objectivity of classification. Instead of answering the question, you respond with your own question, then get upset that we didn’t answer your question, but redirected you back to the original discussion.

  23. keiths: The removal of a constraint does not compel a designer to adopt any particular style of design. It simply means he can operate without being bound by that constraint.

    A good designer is voluntarily bound by constraints like continuity and flow. A bad designer not so much.

    The best designers do new and surprising things while not sacrificing continuity and flow.

    keiths: I know your impulse is to disagree without understanding, but try to suppress that urge and approach this rationally, instead.

    It’s not about disagreeing.

    If I was to play god and start from scratch with no ancestor/descendant constraints and design a “biologic totality” for humans to exercise stewardship over it would look a lot like the one we see except perhaps for the cats. 😉

    You might choose to do it differently I suppose but I don’t see your personal preference as any kind of argument against “common design”

    peace

  24. fifthmonarchyman: Again we have moved beyond mere common descent to something approaching full blown Darwinism.

    Full blown Darwinism includes natural selection, which is not relevant here. All we have here is branching descent and variation.

    fifthmonarchyman: However i’m interested in the nested hierarchy’s relationship with common descent in isolation. Is there any evidence for that?

    The nested hierarchy is entailed in branching descent with variation. We observe the nested hierarchy, supporting the hypothesis.

    fifthmonarchyman: and wouldn’t something like discrete creation events utilizing information and raw materiel from preexisting populations also lead to a nested hierarchy?

    Humans designs rarely form objective nested hierarchies. That’s because designs don’t branch neatly, but are subject to rampant crossings, as well as saltation.

    fifthmonarchyman: Before you go off half-coked I’m not saying that is what happened I just trying to understand why nested hierarchy uniquely suggests common descent to you.

    Because it is a necessary deduction from the hypothesis.

    fifthmonarchyman: If that is correct then the tree of life is clearly not a nested hierarchy.

    The leaves on the tree of life do form a nested hierarchy, with some exceptions.

    fifthmonarchyman: we assume that eukaryotes arose from the union of two different kingdoms anaerobic archaea and respiring alpha-proteobacteria

    That’s right. As Darwin noted, the tree is not perfect. However, for the vast majority of organisms, the signal for the tree is very distinct. This is the pattern that looks for explanation.

    fifthmonarchyman: An anatomist can objectively recognize a bird if what she sees is in fact a bird.

    And other careful observers agree.

    objective, of, relating to, or being an object, phenomenon, or condition in the realm of sensible experience independent of individual thought and perceptible by all observers

    fifthmonarchyman: Given atheism I just don’t see how she can demonstrate that what she thinks she sees is objective reality.

    Are these in tension?

    fmm: An anatomist can objectively recognize a bird if what she sees is in fact a bird.

    fmm: Given atheism I just don’t see how she can demonstrate that what she thinks she sees is objective reality.

    Trying to parse your two statements according to your thinking, biologists can objectively recognize the nested hierarchy, but can’t demonstrate that it is objective. Of course, it doesn’t matter, as long as observers agree that the pattern is objective, which you agree is possible.

    Consequently, your argument isn’t about the nested hierarchy, but about whether we can objectively say that birds have feathers.

  25. fifthmonarchyman: and wouldn’t something like discrete creation events utilizing information and raw materiel from preexisting populations also lead to a nested hierarchy?

    Mung: John has already said it would. Perhaps the zachriels will disagree.

    Humans don’t design that way, but it is possible to conceive of a designer that prunes the tree of life into a preferred shape (or “lovingly crafts each and every mutation”). As long as we have branching descent with variation, the result will be a nested hierarchy.

  26. keiths:

    You’re making a silly logic mistake. The removal of a constraint does not compel a designer to adopt any particular style of design. It simply means he can operate without being bound by that constraint.

    fifth:

    A good designer is voluntarily bound by constraints like continuity and flow. A bad designer not so much.

    As I said:

    And one can easily show respect for conventions, such as the QWERTY keyboard layout, without being bound by ancestor-descendant relationships.

    Do you see your mistake?

  27. fifthmonarchyman: it’s not confusion

    The “nest” we put crows into depends on the attribute we are focusing on. If we are looking at the feathers attribute they are placed in the birds nest if we are looking at diet the fit into the “omnivores” nest, if we are looking at walking legs they fit into the “bipedal” nest.

    Yup. Thank you for confirming my original suspicion that the member/attribute confusion is intentional.

    But even granting your point for the sake of argument what “nest” does lichen fit into? What about the Beefalo? the Lonicera fly? the Mariana mallard? The Red wolf?

    Depends: fungus/plant or fungus/cyanobacter symbiote, bovidae, rhagoletis, anas, and canis, respectively.
    Why do you ask?

    More fundamentally since presumably eukaryotes arose from a merger of Proteobacteria and Archaeans what ancestral nest do we fit in?

    Glad you agree to sensibly presume that we arose via endosymbiosis. That may qualify as the most reasonable presumption you have ever made. It’s a low bar.
    Oh, we’re primates.

  28. Zachriel: The leaves on the tree of life do form a nested hierarchy, with some exceptions.

    and

    Zachriel: That’s right. As Darwin noted, the tree is not perfect.

    and

    Zachriel: Humans designs rarely form objective nested hierarchies.

    No humans designs form “not perfect” objective nested hierarchies “with some exceptions”.

    It seems to me that all this comes down to your judgeing one nested hierarchy to be good and another bad.

    Then declaring your opinion “objective”

    I would say that if the nested hierarchy we see in the tree of life is somehow better than the one we could come up with it’s just means that God is a better designer than us.

    peace

  29. fifth:

    If I was to play god and start from scratch with no ancestor/descendant constraints and design a “biologic totality” for humans to exercise stewardship over it would look a lot like the one we see except perhaps for the cats.

    Why? Why would you slavishly adhere to ancestor-descendant constraints that aren”t needed or beneficial? That’s bad design.

  30. Sigh. Still think It’s better to go with molecular characters. Then you don’t get spurious attempts to cast doubt on hierarchy by such facts as birds being ‘bipedal’. Molecular character states are studiously avoided by Creationists for a reason.

  31. fifthmonarchyman: A lung of a mouse is pretty similar to the lung of an elephant or the lung of a human so you don’t have to start from scratch to understand the workings of each and every animal you encounter.

    That is a great gift and the hallmark of good design

    Why is either true?

    More importantly, why are bird lungs fairly different, and really better? Bird lungs are not a great gift to mammals, nor are mammalian lungs the hallmark of good design.

    What we do have with bird lungs and mammal lungs is the familiar restriction of adaptations to particular lineages. Almost as they evolved in one line and no one thought to share the “technology,” like an actual designer typically would.

    Someone like colewd all of a sudden gets concerned about holistic issues whenever serious issues arise for “design,” like where mammalian testes typically have to descend to the scrotum. Never ever does it bother him in the least when he’s claiming “good design,” it’s just all of a sudden complex and has to be worked out entirely to when one shows that some dumbass “idea” like continuing to develop testes in the near-ancestral position then moving it is not a great idea, not that making mammals need lower temps for testes is a good idea in the first place (bird testes don’t). He can just look at bird flight and know that it must have been designed, don’t you know. Complete double standards, but there you go, no details have backed up any of his non-trivial claims, and his “nested hierarchy” of “Apple computers” has never even been diagrammed or otherwise demonstrated in the least, only asserted and endlessly reasserted.

    Glen Davidson

  32. keiths: Why? Why would you slavishly adhere to ancestor-descendant constraints that aren”t needed or beneficial?

    Continuity and flow are beneficial and needed.

    In fact I would say they a crucial for understanding.

    A world with out continuity and flow would appear random and would certainly be incomprehensible.

    peace

  33. fifthmonarchyman: No humans designs form “not perfect” objective nested hierarchies “with some exceptions”.

    No. Human artifacts simply don’t form into objective nested hierarchies. With human artifacts, we can form many different equally valid classification schemes.

    fifthmonarchyman: It seems to me that all this comes down to your judgeing one nested hierarchy to be good and another bad.

    No. We can quantify the fit to the nested hierarchy, especially so with genetics.

    fifthmonarchyman: Then declaring your opinion “objective”

    objective, of, relating to, or being an object, phenomenon, or condition in the realm of sensible experience independent of individual thought and perceptible by all observers.

  34. fifthmonarchyman: It seems to me that all this comes down to your judgeing one nested hierarchy to be good and another bad.

    Are you still arguing that careful observers, considering all the various objective traits of crows, sparrows, and humans, would not place crows and sparrows together apart from humans?

    {{crows, sparrows}, humans}

  35. GlenDavidson: More importantly, why are bird lungs fairly different, and really better?

    again with the personal opinions.

    I think bird lungs are good for birds. and mammal lungs are good for mammals

    GlenDavidson: like where mammalian testes typically have to descend to the scrotum. Never ever does it bother him in the least when he’s claiming “good design,”

    I think that descended testes are a great design for humans.

    GlenDavidson: not that making mammals need lower temps for testes is a good idea

    Changing the overall temps just for testes is a bad idea when simply descending them will do just fine.

    peace

  36. Zachriel: Are you still arguing that careful observers, considering all the various objective traits of crows, sparrows, and humans, would not place crows and sparrows together apart from humans?

    That was never my argument.

    strike two and a half 😉

    Popular does not mean objective.
    “Careful” is in the eye of the beholder unless you have a standard of comparison

    peace

  37. fifthmonarchyman: That was never my argument.

    Can we objectively say that crows have feathers?

    If yes, then can we objectively observe a large number of traits of crows, sparrows, and humans?

    If yes, then considering all the traits, would the vast majority of those traits (bones, lungs, brain, skin, blood cells, thousands of points of genetic similarities and differences) lead someone to place crows and sparrows together apart from humans?

  38. PopoHummel: The letters on my computer keyboard are arranged in a QWERTY pattern not because the designer had to do it that way or because he was constrained by some sort of “ancestor-descendant relationship” but because it’s familiar to me and therefore I didn’t have to learn an entirely new pattern in order use it.

    Yes, that’s why “QWERTY” is about all that is the same in today’s computer keyboards as in the layout of ancient mechanical typewriters. Today’s keyboards are electronic, many connected to the computer by nothing but a radio connection, while mechanical typewriters, well, were all about mechanical linkages.

    Today’s keyboards wouldn’t fool any systematist. There’s some continuity, but that’s clearly not some sort of requirement, indeed, people convert to Dvorak or Azerty (for instance) relatively easily (except possibly for the learning curve). Your point about QWERTY is the exception of continuity that indicates how different the rules actually are, since the QWERTY layout is simply one choice among many, usually chosen for familiarity. Practically everything else about the keyboards is not traditional to mechanical typewriters.

    You pick and choose technologies and layouts according to convenience and need, not like organisms, which are constrained to modifying past structures inherited from their ancestors.

    Glen Davidson

  39. fifth:

    Continuity and flow are beneficial and needed

    Slavish adherence to ancestor-descendant constraints is not needed. That’s why human designs don’t fall into objective nested hierarchies, colewd’s goofy claims notwithstanding.

    If human designers have figured this out, why can’t God? Whence his low intelligence?

  40. Zachriel: No. Human artifacts simply don’t form into objective nested hierarchies.

    According to whom? and who made them king?

    Zachriel: With human artifacts, we can form many different equally valid classification schemes.

    The same goes with life it depends on the attributes we want to focus on.

    Focus on diet get one scheme focus on size get another.

    Zachriel: objective, of, relating to, or being an object, phenomenon, or condition in the realm of sensible experience independent of individual thought and perceptible by all observers.

    right your opinion is never independent of your thought and all observers don’t perceive it is correct in this instance.

    peace

  41. fifthmonarchyman: again with the personal opinions.

    I think bird lungs are good for birds. and mammal lungs are good for mammals

    I think that descended testes are a great design for humans.

    Changing the overall temps just for testes is a bad idea when simply descending them will do just fine.

    peace

    Wow, you baptize everything about life as just peachy (with perhaps some “curse” exceptions or what-not).

    The double standard again (if it’s good, well, it’s just obvious that it’s good, and if it’s bad, well, it’s really good if you are “deep” or some such rot), the circular thinking. I didn’t expect something better from you, though, so not a disappointment.

    Glen Davidson

  42. fifthmonarchyman: According to whom?

    According to the evidence.

    fifthmonarchyman: The same goes with life it depends on the attributes we want to focus on.

    That is not correct. When we look at ALL the evidence, crows and sparrows group together with humans outside.

    fifthmonarchyman: Focus on diet get one scheme focus on size get another.

    But if you focus on ALL the evidence, you get an objective nested hierarchy.

  43. GlenDavidson: Wow, you baptize everything about life as just peachy (with perhaps some “curse” exceptions or what-not).

    I’m generally a cockeyed optimist.
    Why is ungrateful nitpicking a better perspective?

    GlenDavidson: The double standard again (if it’s good, well, it’s just obvious that it’s good, and if it’s bad, well, it’s really good if you are “deep” or some such rot)

    Actually I know it’s good because I know the designer loves me and works everything for my good even things that don’t appear to be good at first glance.

    It’s not circular thinking it’s thinking based on my personal knowledge of the designer’s power and intention toward me.

    peace

  44. fifthmonarchyman: Are you saying an observer could understand a “stone lung” as quickly and easily as one that is similar to those he had already encountered?

    No.

    Yes, I would suppose that if the design requirement is that the world be borderline incomprehensible to us then we would not expect a nested hierarchy.
    or any discernible pattern at all for that matter.

    Since our ability to understand the world is not at all a concern of darwininistic evolution it’s very lucky that things turned out they way they did.

    One could also argue it’s not lucky that things turned out the way they did. I can imagine a worse outcome and I can imagine a better outcome…

    My only problem with your posting was the term “good design”.

  45. Zachriel: According to the evidence.

    judged by whom?

    Zachriel: When we look at ALL the evidence, crows and sparrows group together with humans outside.

    How do you know you have ALL the evidence? How do you determine the relative importance of each individual piece of evidence?

    Who decided crow’s feathers should be given more relative weight than their understanding of analogy

    https://www.scientificamerican.com/article/crows-understand-analogies/

    peace

  46. PopoHummel: My only problem with your posting was the term “good design”.

    I agree good is in the eye of the beholder.
    When I say good I generally mean good for me

    peace

  47. fifthmonarchyman: I’m generally a cockeyed optimist.
    Why is ungrateful nitpicking a better perspective?

    Analysis is better because it yields results based on the evidence. Ungrateful nitpicking is what you do any time you’re confronted with evidence against your claims.

    Actually I know it’s good because I know the designer loves me and works everything for my good even things that don’t appear to be good at first glance.

    It’s not circular thinking it’s thinking based on my personal knowledge of the designer’s power and intention toward me.

    Not about to question the dogmas taught to you. It might lead to thinking that is open-ended.

    Glen Davidson

  48. fifthmonarchyman: judged by whom?

    By independent statistical analysis, if you want.

    fifthmonarchyman: How do you have ALL the evidence?

    All the {available} evidence.

    fifthmonarchyman: Who decided crow’s feathers should be given more relative weight than their understanding of analogy

    We have thousands of points of comparison. Use any reasonable criteria. Or use genetic comparison.

    Can we objectively say that crows have feathers?

  49. Zachriel: Can we objectively say that crows have feathers?

    You can objectively say crows have feathers if it can be known for certain that in fact crows have feathers.

    I’m not sure how an atheist can say any thing objectively.

    You can say that it appears to you that crows have feathers or the folks you know about claim to agree that crows have feathers. Something like that.

    If God does not exist then there there is no perspective that is free from personal bias and limitations.

    peace

  50. Zachriel: By independent statistical analysis, if you want.

    Ok

    When it comes to crows sparrows and humans let’s look at relative proficiency in reproducing phrases in human language verses number of feathers on the butt.

    would we get the same tree?

    Zachriel: All the {available} evidence.

    available to whom?

    I have different evidence available to me than you have does that mean we will get different trees?

    you are so tiresome.

    No offense I’m going to temporally put you on ignore for a while. So this conversation doesn’t get bogged down more than it already has.

    peace

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