Phylogenetic Systematics

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. Flint: Macroevolution implies common descent, and vice versa. You’re not going to get one without the other.

    Didn’t you just say you can get one with out the other when it comes to the x86 clade of computer?

    surely no Macroevolution going on there

    Flint: If you are focusing on the structure of the tree, you’d look at macroevolution. If you are focusing on the growth process of the tree, you’d look at common descent.

    I’d argue that the structure was the result of common descent and Macroevolution/Darwinism is one explanation for the growth process of the tree.

    But I do think you make an interesting point.

    peace

  2. fifthmonarchyman:What exactly separates Darwinism from common descent or are they a irreducibly complex package deal IYO?

    peace

    Strict Darwinism holds that new species originate entirely through a combination of variation and selection. If this were the whole picture, common descent would follow. However, there are other mechanisms (like drift) of which Darwin was unaware. When drift is included, common descent STILL follows.

    Maybe it would be helpful to say that common descent is a logical entailment of a large body of observations. It’s something that IS. What Darwin and others have constructed is a proposed set of mechanisms which together produced this condition. You should never confuse an observation with an explanation.

  3. fifthmonarchyman: Didn’t you just say you can get one with out the other when it comes to the x86 clade of computer?

    Yes, you CAN in theory. But it doesn’t generally happen in practice, for practical reasons. Whereas in biology, there’s no way to get around it.

  4. Flint: Provided you understand why it’s not a really good analogy. (Hint: it’s not a good analogy because computers do not breed.)

    I guess it depends on what you mean by breed. 😉

    You can stretch any analogy beyond it’s usefulness.
    The key to to use them to their fullest but not beyond it

    peace

  5. Flint: Whereas in biology, there’s no way to get around it.

    That my new favorite, is a debate for another time.

    peace

  6. fifthmonarchyman: I’d argue that the structure was the result of common descent and Macroevolution/Darwinism is one explanation for the growth process of the tree.

    I was thinking, if you view the structure of a tree as branches off of branches off of branches, you are looking at macroevolution (trunk to thick branch to twig, etc.) If you look at the whole tree altogether, every twig leaf and trunk and branch, you see one single object, descended from a common seed.

  7. Flint: You should never confuse an observation with an explanation.

    thank you
    in computers and life we observe a nested hierarchy.

    The explanation is another kettle of fish.

    Flint: Maybe it would be helpful to say that common descent is a logical entailment of a large body of observations.

    This sounds like the beginnings of an actual argument at last.

    Can you please give a short summery of the observations and explain why common descent is a logical entailment of them.

    It would sure make this thread end better than it started

    thanks in advance

  8. Flint,

    Since this is the field we both have been in, probably for decades…

    Processor design is my field, but it doesn’t appear to be yours. Judging by your comments, you are a software person, not a processor designer.

    Why not take your own advice, which was:

    You should tread more carefully in territory outside your field.

  9. John Harshman:
    I think you’re confused about what causes we’re talking about here. The causes of the ink marks are not relevant. It’s the nested hierarchy of ink marks in different copies that counts, and that’s explained by imperfect copying of manuscripts from prior manuscripts. Similarly, in life, it’s not the causes of differences that counts, it’s the nested hierarchy of differences, and that’s explained by imperfect copying of populations (and individuals) from prior populations (and individuals).

    Yes, I got it: Just the nested hierarchy is relevant, i.e. the effects, not causes. The problem with this is that it’s just you (and Felsenstein) saying this. Other evolutionary biologists are quite able to talk about causes. In fact even you are, occasionally, randomly, in contradiction to yourself.

    John Harshman:
    The analogy breaks down first in your misunderstanding of where the analogy lies, i.e. your misplaced focus on the causes of ink marks, and second in the different modes of replication between manuscripts and populations.

    The analogy may have broken down already when you failed to detail to what extent it applies, if at all. If you fleshed it out properly, it would also nicely elucidate how much you understand about textual analysis.

    John Harshman:
    I will assume that your confusion of what causes are relevant here is unfeigned. We know the causes of nested hierarchy.

    Heh, see, now you know the causes. Then what was that above about causes not being relevant?

    John Harshman:
    We know some of the causes of changes, but by no means all of them, but those aren’t relevant in explaining nested hierarchy. But Incidentally, if you flounce and then keep going, that detracts from the credibility of the flounce. Best save it for the end.

    As long as you are not stating the causes of the nested hierarchy, in what sense do you think you are explaining the nested hierarchy? Only in a very limited sense. Absent explicit sufficient causes, the explanation is by necessity compatible with a wide range of causes, including designers and what not, particularly given the analogy. Not much of an explanation, sorry.

    John Harshman:
    We don’t have to know the causes of differences. We can infer the causes of nested hierarchy.

    And here you say we don’t have to know the causes again. Given your self-contradiction, I don’t trust you to infer much.

    John Harshman:
    Fortunately, there are rational reasons for believing it: nested hierarchy, fossil record, biogeographic patterns, etc. Mind you, this says nothing about the causes of mutation.

    That’s what I keep saying: All this says nothing about causes. So why not focus on finding them, instead of flouncing? First you say that causes are not relevant, then that you know some of them, and then that you have an explanation regardless of knowing the causes. Srsly.

  10. fifthmonarchyman: It’s really just about getting clarification of the terms you are using in your argument. It’s not a strategy at all.

    It is not the what but the how which is the strategy, Fifth. Why inject one’s relationship with a possible divine into a clarification of what criteria are used to construct an “objective nested hierarchy” ?

    As I repeatedly said I do not want this thread to get mired in a philosophical ditch.

    I agree you have repeatly said that, it is your inability to answer a simple question whether crows have feathers without jerking the wheel towards you favorite subject,

    “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.”

    And this is how you avoid a philosophical ditch? Good job.

    peace

  11. fifthmonarchyman: Right, If objectivity is logically impossible then it necessarily does not exist.

    or if a perfect circle does not exist we cannot say anything is a ⭕️ ?

    But in that case any conclusion of that nature would necessarily be just my own subjective opinion. There would be no way to know for sure

    And not even omniscience and omnipotence would able to overcome the logical restraints no matter how much one presupposed it could.

    😉

    peace

  12. Erik: Yes, I got it: Just the nested hierarchy is relevant, i.e. the effects, not causes.

    You have to stop referring to “causes” without considering what causes you’re talking about. Some causes cause nested hierarchy, and other causes cause mutation and fixation and speciation. They aren’t the same causes. You are hiding behind a single word that covers both relevant and irrelevant matters.

    The analogy may have broken down already when you failed to detail to what extent it applies, if at all. If you fleshed it out properly, it would also nicely elucidate how much you understand about textual analysis.

    I don’t see where you’re confused. Scribes, many of them illiterate, copied manuscripts, made copying errors. Later scribes copied the manuscripts, including the existing errors, and made errors of their own, which were copied by later scribes. Errors in common among manuscripts allow us to determine common descent of copies. Here is a more elaborate explanation of the analogy: Howe C.J., Barbrook A.C., Spencer M., Robinson P., Bordalejo B., Mooney L.R. Manuscript evolution. Trends in Genetics 2001; 17:147-152.

    Heh, see, now you know the causes. Then what was that above about causes not being relevant?

    Please read entire sentences and paragraphs, not just a couple of words. The causes of nested hierarchy are relevant to explaining nested hierarchy. The causes of other things are not relevant to explaining nested hierarchy. You don’t have to know why a scribe made a particular error in order to find the descent of manuscripts. You don’t have to know why mutation, fixation, and speciation happen in order to find the descent of species. We do know a lot about those things, but it isn’t relevant to the current subject.

    As long as you are not stating the causes of the nested hierarchy, in what sense do you think you are explaining the nested hierarchy?

    I am stating the causes of the nested hierarchy, so your question rests on a false premise.

    And here you say we don’t have to know the causes again. Given your self-contradiction, I don’t trust you to infer much.

    Giver your inability to read what I’ve said, your ability to recognize self-contradictionk shouldn’t be trusted. You consistently hide behind “the causes” without specifying what they’re causes of, as if there were a unitary block of causes all of which must be invoked to explain anything. Newton explained the orbits of the planets by his theory of universal gravitation. Your claim seems to be that gravity doesn’t exist because Newton didn’t know what causes gravity, or what particles make up matter, or how the planets formed, or whether there are planets around other stars.

    That’s what I keep saying: All this says nothing about causes. So why not focus on finding them, instead of flouncing? First you say that causes are not relevant, then that you know some of them, and then that you have an explanation regardless of knowing the causes. Srsly.

    You don’t appear to know what “flouncing” is. It’s the claim to be ending a discussion, taking your toys, and going home. You do it a lot. I didn’t do it above. Anyway, I will repeat my point as clearly as I can, in hopes that you will read for comprehension this time.

    There are a great many causes in the world. Only a few of them are relevant to the understanding of nested hierarchy. The causes of nested hierarchy are reproduction, splitting of lineages, and changes within lineages. As long as these three things happen and the last is not so great as to erase all prior information, there will be a nested hierarchy. It isn’t necessary to know the causes of the causes, i.e. the causes of reproduction, splitting, and change in order to determine that the causes have been operating. You are confusing the causes of nested hierarchy with the causes of the causes of nested hierarchy. That creates an infinite regress that’s irrelevant to the subject. It happens that we do know quite a bit about the causes of the causes of nested hierarchy, but that’s a different subject.

    So, did any of that confuse you?

  13. newton: Why inject one’s relationship with a possible divine into a clarification of what criteria are used to construct an “objective nested hierarchy” ?

    Claiming that your aprasial is objective while mine is merely subjective strikes me as domineering. When you do so I what to know who your authority is

    newton: I agree you have repeatly said that, it is your inability to answer a simple question whether crows have feathers without jerking the wheel towards you favorite subject,

    the question wasn’t “do crows have feathers”
    the question was “do crows objectively have feathers”

    It’s more about the nature of reality than about crows.

    newton: And this is how you avoid a philosophical ditch? Good job.

    The way to avoid a philosophical ditch is simply provide a definition of “objective” that does not implicitly invoke the divine.

    Do that and we would be good.

    newton: or if a perfect circle does not exist we cannot say anything is a ⭕️ ?

    You can say something resembles a perfect circle

    You just can’t say your determination is objective unless you define objective in a way that does not exclude your personal bias.

    got it?

    newton: And not even omniscience and omnipotence would able to overcome the logical restraints no matter how much one presupposed it could.

    that’s just your subjective personal opinion right? 😉

    seriously, It’s more about “perfectly just” than it is about omnipotence

    peace

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

    I actually agree with that. However the “if God does not exist” part is a red herring. Regardless of whether God exists, there is no human perspective that is free from personal bias and limitations.

  15. Neil Rickert: Regardless of whether God exists, there is no human perspective that is free from personal bias and limitations.

    Thank you. You are back to being my favorite.

    peace

  16. Neil Rickert: Regardless of whether God exists, there is no human perspective that is free from personal bias and limitations.

    As Douglas Adams said, “The fact that we {humans} live at the bottom of a deep gravity well, on the surface of a gas covered planet going around a nuclear fireball 90 million miles away and think this to be normal is obviously some indication of how skewed our perspective tends to be.”

    Nevertheless, there is a difference between the assertion “Crows have feathers”, and “Led Zeppelin is the greatest rock band ever”. If the term ‘objective’ represents an unattainable binary, rather than something achieved in degrees, then we need another word for the distinction.

    The primary question of the thread concerns the ‘objective nested hierarchy’. The modifier is chosen to distinguish it from arbitrary nested hierarchies, such as library classification schemes.

  17. Zachriel: The primary question of the thread concerns the ‘objective nested hierarchy’. The modifier is chosen to distinguish it from arbitrary nested hierarchies, such as library classification schemes.

    Library classification schemes are as objective as biological classification schemes.

  18. Neil Rickert: Library classification schemes are as objective as biological classification schemes.

    Biological cladistics are based on objective independently verifiable observable traits of organisms, all pointing to a single hierarchical nesting. Not so with library classification schemes, which can be changed from one to another with equal validity.

  19. Zachriel: Nevertheless, there is a difference between the assertion “Crows have feathers”, and “Led Zeppelin is the greatest rock band ever”. If the term ‘objective’ represents an unattainable binary, rather than something achieved in degrees, then we need another word for the distinction.

    I think that this is the key philosophical point: we need a way of thinking about objectivity as achievable in degrees and not as absolute (since the absolutely objective is not just unattainable practically but cognitively empty for us).

  20. Kantian Naturalist: I think that this is the key philosophical point: we need a way of thinking about objectivity as achievable in degrees and not as absolute (since the absolutely objective is not just unattainable practically but cognitively empty for us).

    You seem to be seeking the scientific method, considered broadly. Here, the key idea is the recognition of the hurdles to achieving objectivity, so that they can be overcome to an extent sufficient to make progress. Maybe we can’t be “truly objective”, but we can deploy peer review, replication, intersubjective consensus, appropriate instrumentation, logical consistency, etc. to help us along.

    And working against this process is the “post truth” mentality, where preference trumps reality, and funding is provided in exchange for politically desired results.

  21. Zachriel: Biological cladistics are based on objective independently verifiable observable traits of organisms, all pointing to a single hierarchical nesting.

    Fair enough.

    I would suggest, however, that the “pointing to” part is a matter of pragmatics rather than a matter of truth.

    One could come up with very different biological classification systems. But they would not be nearly as useful.

  22. Kantian Naturalist: I think that this is the key philosophical point: we need a way of thinking about objectivity as achievable in degrees and not as absolute (since the absolutely objective is not just unattainable practically but cognitively empty for us).

    I think we are far enough along to practically distinguish between statements of the form “Led Zeppelin is the greatest rock band ever” (which we understand is a universal objective truth that brooks no argument), and “Crows have feathers” (the antonym of objective being subjective).

    Flint: Maybe we can’t be “truly objective”, but we can deploy peer review, replication, intersubjective consensus, appropriate instrumentation, logical consistency, etc. to help us along.

    And making predictions about seemingly unrelated phenomena, such as the lengthened half-life of accelerated particles from the constancy of the speed of light; the retardation of the pendulum from the hypothesized movement of the Earth; or fossils (rocks) from the pattern of extant organisms.

  23. Neil Rickert: I would suggest, however, that the “pointing to” part is a matter of pragmatics rather than a matter of truth.

    Put the observable traits in a statistical blender, and you always get the same nested hierarchy. That’s what is meant by a objective nested hierarchy (of observable traits).

  24. Flint: Maybe we can’t be “truly objective”, but we can deploy peer review, replication, intersubjective consensus, appropriate instrumentation, logical consistency, etc. to help us along.

    I think we need a realization that this is about all that “objective” could mean to us. There’s too much of a tendency to idealize “objective” to be something that could not actually exist.

    And working against this process is the “post truth” mentality, where preference trumps reality, and funding is provided in exchange for politically desired results.

    I’m certainly not for a “post truth” mentality.

    Much as people have idealized “objective” to something that could not possibly exist, they have idealized “truth” to something that could not exist. The “post truth” mentality is a reaction to an over-idealized notion of “truth”.

    Maybe we just need to be more realistic.

  25. Zachriel: Put the observable traits in a statistical blender, and you always get the same nested hierarchy. That’s what is meant by a objective nested hierarchy (of observable traits).

    You could come up with a objective nested hierarchy for biology, based entirely on color (which I take to be an observable trait). What you would get would not be the same nested hierarchy. But it also would not be very useful.

  26. Neil Rickert: One could come up with very different biological classification systems. But they would not be nearly as useful.

    “useful” is very context dependent. Useful in one situation might be useless in another.

    If I’m a zoo keeper working to build an efficient operation classifying by size or diet would certainly be more useful than classifying by genetic similarity.

    No matter how you slice it it’s impossible for us humans to get beyond individual subjective choice.

    peace

  27. Neil Rickert: But it also would not be very useful.

    I think this is a great point.

    Do you want to know why life forms a nested hierarchy.

    It does so because that pattern is most useful to facilitate human understanding

    I find that to be incredibly providential. (Atheists would say lucky)

    peace

  28. fifthmonarchyman: “useful” is very context dependent. Useful in one situation might be useless in another.

    I agree with that.

    No matter how you slice it it’s impossible for us humans to get beyond individual subjective choice.

    However, here I disagree.

    Intersubjective agreement already gets us beyond individual subjective choice.

  29. Neil Rickert: Intersubjective agreement already gets us beyond individual subjective choice.

    How many subjects are involved in the agreement? What are their biases?

    If it is not all possible subjects or if the subjects are biased in some way then you are back to popularity and individual subjective choice.

    peace

  30. Neil Rickert: You could come up with a objective nested hierarchy for biology, based entirely on color (which I take to be an observable trait).

    If you put observable colors into a statistical blender, you would find many different nested hierarchies that have similar fits. Many other traits, however, would mirror the nested hierarchy for all traits.

    fifthmonarchyman: If I’m a zoo keeper working to build an efficient operation classifying by size or diet would certainly be more useful than classifying by genetic similarity.

    Sure. But when you consider all the known traits, there is an exceedingly strong signal of a specific nested hierarchy.

  31. fifthmonarchyman: If it is not all possible subjects or if the subjects are biased in some way then you are back to popularity and individual subjective choice.

    People can reach intersubjective agreement on what they are talking about, while still disagreeing about their conclusions.

  32. keiths, to fifth:

    Given the supreme incompetence you just demonstrated, why are you giving any credence to your objections? Theobald is a smart guy. You are functioning so far below his level that you couldn’t even grasp the meaning of his title, much less the contents of the article itself.

    Lots of incompetent people will come up with lots of stupid objections to things that they don’t understand. You are one of those people. Don’t waste time on those stupid objections.

    Focus on the good stuff, which Theobald has graciously provided to you, instead of the objections of an incompetent and disorganized mind — yours.

    You are here to learn. You are not in a position to challenge, because you don’t even understand the material. Follow the example of brighter folks: learn first, and once you understand, then challenge if you think you have a case.

    You keep doing it backwards, and it wastes everyone’s time.

    fifth:

    They are more questions than objections.

    No, they are objections, like arguing against Theobald’s title in a lame attempt to cover your mistake. Don’t waste any time on them. They’re coming from a guy who can’t even read and comprehend the title of Theobald’s article, much less its content; a guy who inadvertently defeated his own argument regarding theism and objectivity; and a guy who has a history of mangling even the simplest of concepts.

    Here’s an analogy: It’s as if you’re enrolled in a class being taught by Theobald, and every day, instead of attending lecture, you spend the time talking to a drunk guy who knows nothing about biology and couldn’t reason his way out of a paper bag (including the one surrounding the bottle he’s drinking from), but has strong opinions on common descent, which he totally misconstrues.

    The bright students waste no time on such discussions. You, being far less intelligent than they, can’t afford to skip class, yet you do, spending the time talking with the drunk guy. His objections are really important, you think, and so you skip class, day after day, learning nothing.

    But he doesn’t know what he’s talking about, and his objections are a complete waste of time. You can’t afford that. You’re struggling just to stay afloat in this class, and the smarter students are leaving you in the dust.

    Now in reality, of course, you aren’t getting the objections from some incompetent drunk guy. But you are getting them from someone who is incompetent and confused, with a history of wasting everyone’s time on worthless digressions. That person, of course, is you.

    Ignore that guy, and pay attention to Theobald. Theobald has much to teach you, and the dumb guy is just holding you back and wasting your time.

    As I recommended earlier:

    Follow the example of brighter folks: learn first, and once you understand, then challenge if you think you have a case.

    You’re nowhere close to understanding at the moment, so your challenges are useless. The order is important: Learn first, and then challenge, if you think you have a case.

  33. Case in point. You write:

    You can choose to not answer questions if you like but If you don’t I will assume that you think they are the same

    Think about how stupid it would be to assume that. It’s an idiotic idea. Why give any credence to it, or to the guy who produced it — a guy who continually produces ideas of similar low quality? You’re not going to learn anything useful from him. He’s a waste of time.

    Ignore him, and focus on Theobald’s article.

  34. Neil Rickert: People can reach intersubjective agreement on what they are talking about, while still disagreeing about their conclusions.

    in a sense yes I suppose,

    In this tread we can agree that we are talking about evolution or objectivity for example but that does not mean that we are in fact talking about the same things.

    Don’t you agree? 😉

    however

    The important question is, Does agreement equal objectivity.
    I don’t think it does.

    peace

  35. keiths: Ignore him, and focus on Theobald’s article.

    Sounds like pretty good advice for some one who does not want interact with those who disagree.

    Lots of my fundamentalist friends recommend that we just ignore the enemies of God because they are so often wrong and focus on the scriptures.

    same principle I guess 😉

    peace

  36. fifthmonarchyman: In this tread we can agree that we are talking about evolution or objectivity for example but that does not mean that we are in fact talking about the same things.

    Agreed. But then we have not reached intersubjective agreement on what we are talking about. Just using the same words is not enough.

  37. Neil Rickert: But then we have not reached intersubjective agreement on what we are talking about.

    I would truly like to explore the concept of actual verses apparent intersubjective agreement and how we can know if we have achieved the former.

    It sounds fun. You should start a thread sometime.

    peace

  38. fifth,

    Sounds like pretty good advice for some one who does not want interact with those who disagree.

    Which isn’t my position at all, of course. It must feel good to lie about your opponents, considering how often you do it. You’re a real gem, fifth, bringing great glory to Jesus with your dishonesty.

    My actual recommendation was quite clear:

    Follow the example of brighter folks: learn first, and once you understand, then challenge if you think you have a case.

    I’m quite happy to discuss this with people who disagree and understand the concepts. You haven’t even begun to understand them, as you’ve so vividly demonstrated.

    Learn first, then challenge. Stop wasting everyone’s time with dumb challenges that simply reflect your ignorance and incompetence. You’re here to learn, and only after learning, at a minimum, will you be in a position to challenge.

  39. Another example. Fifth writes:

    Do you want to know why life forms a nested hierarchy.

    It does so because that pattern is most useful to facilitate human understanding

    Says fifth, who is baffled by the pattern and does not understand its defining characteristics.

    So God screwed up and picked a pattern — the objective nested hierarchy — that Sal, Bill, fifth, and Mung can’t even begin to grasp. Because that is “most useful to facilitate human understanding.”

    Fifth, you’re just producing one stupid idea after another. If you want to learn this stuff, then you really need to ignore yourself and focus on Theobald.

  40. Flint,

    I think two things are happening here. One is your consistent overweening condescension toward anything that sounds like disagreement (a very Trumpian “why discuss when you can attack” philosophy)…

    It’s amusing that you would invoke Trump, considering how Trump-like your own behavior has been.

    Consider:

    1) You assumed, for no reason, that processor design was not my field of expertise, and that you knew more about it than I did — an assumption that backfired badly on you;

    2) You piously dispensed advice (“You should tread more carefully in territory outside your field”), which you failed to apply to yourself, leading to an embarrassing mistake;

    3) Instead of acknowledging your mistakes, you tried to evade responsibility for them;

    4) You tried to smear your opponent, when in fact it was your own behavior that was questionable.

    That’s all quite Trump-like, isn’t it? You can’t feel very good about that, considering the disdain you expressed for Trump earlier.

    Why not learn to evaluate yourself more realistically? And to acknowledge mistakes, and to rein in your ego? And to take your own advice about treading carefully in fields outside your expertise?

    It will lead to less embarrassment in the new year.

  41. colewd:

    Why do you think that computers are following this path of heredity and cars are not?

    Neither cars nor computers form objective nested hierarchies. Living things and natural languages do. You still don’t get what an objective nested hierarchy is.

    The 80386 was similar in architecture to the 80286. The big change was the pentium as I remember.

    That’s completely backwards. The 386 architecture was enormously different from the 286’s, but the Pentium’s was not very different from the 486’s. It was the microarchitectural changes that were most significant in the Pentium — in particular the fact that it was superscalar.

  42. John Harshman: The causes of nested hierarchy are reproduction, splitting of lineages, and changes within lineages. As long as these three things happen and the last is not so great as to erase all prior information, there will be a nested hierarchy.

    So far so good.

    John Harshman:
    It isn’t necessary to know the causes of the causes, i.e. the causes of reproduction, splitting, and change in order to determine that the causes have been operating. You are confusing the causes of nested hierarchy with the causes of the causes of nested hierarchy.

    Ah, so this is where the confusion lies. Namely, your confusion. You have not been reading with comprehension. And here’s a wild prediction: You will not read with comprehension what follows now.

    I am not asking about causes of causes. All along, I have been asking about sufficient causes. I am asking if the causes you listed are sufficient to establish the claimed common descent.

    Let’s concede that reproduction, splitting of lineages, and changes within lineages cause the nested hierarchy. Two questions:
    – Are the listed causes the only possible ones? Are there no more causes than these listed? (This is a relevant question to eliminate competing hypotheses to Darwinian common descent.)
    – Are these causes sufficient to account for the entire extent or scale of the nested hierarchies? The scale is relevant, because it’s the scale that makes Darwinian common descent what it is. Adaptation is trivial. The causes must account for speciation and beyond. Everything beyond speciation is highly interesting, less than that is irrelevant.

    John Harshman:
    That creates an infinite regress that’s irrelevant to the subject.

    Actually, infinite regresses are highly significant. They help detecting false reasoning, incomplete explanations, circularity and the like.

  43. fifthmonarchyman: The important question is, Does agreement equal objectivity.
    I don’t think it does.

    I concur agreement does not equal objective, however if we agree to measure on base percentage as “how often a batter reaches base. It is approximately equal to Times on Base/Plate appearances. The full formula is OBP = (Hits + Walks + Hit by Pitch) / (At Bats + Walks + Hit by Pitch + Sacrifice Flies) “ that is an objective measure. We can objectively assess anyone using that measure.

  44. Kantian Naturalist: I think that this is the key philosophical point: we need a way of thinking about objectivity as achievable in degrees and not as absolute (since the absolutely objective is not just unattainable practically but cognitively empty for us).

    A better expressed version of my point

  45. keiths,

    Neither cars nor computers form objective nested hierarchies. Living things and natural languages do. You still don’t get what an objective nested hierarchy is.

    I think that depends on the definition on objective. If you go by what Newton is suggesting then biology may not make the cut. Based on Theobald’s example computers, or aspects of computers like operating systems, in certain cases can be nested and that nesting is the result of a design tradeoff.

    That’s completely backwards. The 386 architecture was enormously different from the 286’s, but the Pentium’s was not very different from the 486’s. It was the micro architectural changes that were most significant in the Pentium — in particular the fact that it was superscalar.

    Didn’t you see that Flint had already corrected me here?

    Oh, because Flint is a software designer and you are a hardware designer his opinion does not count 🙂

  46. keiths:

    Neither cars nor computers form objective nested hierarchies. Living things and natural languages do. You still don’t get what an objective nested hierarchy is.

    colewd:

    I think that depends on the definition on objective.

    As I said, you still don’t get what an objective nested hierarchy is. Theobald explains the concept quite clearly; I don’t see why you guys have such trouble with it. Focus on his description. If you have trouble with it, ask specific questions, quoting the parts you find difficult to fathom.

    Based on Theobald’s example computers, or aspects of computers like operating systems, in certain cases can be nested and that nesting is the result of a design tradeoff.

    That isn’t what “objective nested hierarchy” means.

    I can’t stress this enough:

    You really, really need to understand what an objective nested hierarchy is if you want to understand why creationism is a crackpot view derided by evolutionary biologists.

    Cars and computers do not fall into objective nested hierarchies. Natural languages and living organisms do.

    All of them can be placed into mere nested hierarchies. That’s trivial, as Theobald explains. What matters is whether they can be placed into objective nested hierarchies. Cars and computers can’t. Natural languages and organisms can.

    Until you grasp this, your struggle will be futile.

    Didn’t you see that Flint had already corrected me here?

    So? Would you characterize yourself as a quick learner who never benefits from repetition?

  47. keiths,

    You really, really need to understand what an objective nested hierarchy is if you want to understand why creationism is a crackpot view derided by evolutionary biologists.

    The objective nested hierarchy is not going to save your myth keiths. It is far too grey to be a measurement you can count on.
    keiths,

    So? Would you characterize yourself as a quick learner who never benefits from repetition?

    On objective information I do pretty well 🙂 Even though calling the change to 32 bits more significant then the move to parallel instructions I can hang with you even if we could access some subjectivity to this opinion.

  48. colewd,

    The objective nested hierarchy is not going to save your myth keiths. It is far too grey to be a measurement you can count on.

    You have a knack for getting things completely wrong. The objectivity of a nested hierarchy can be rigorously quantified, and we’ve already discussed that in this thread. Jesus, Bill.

    On objective information I do pretty well 🙂 Even though calling the change to 32 bits more significant then the move to parallel instructions I can hang with you even if we could access some subjectivity to this opinion.

    You managed to get even that wrong. I didn’t say that one was more significant than the other. I pointed out that superscalarity was a microarchitectural change, not an architectural one. You fail even at basic reading comprehension.

    Honestly, Bill — do you truly think a guy of your modest abilities has spotted errors in the argument for common descent that the entire evolutionary biology has overlooked? Don’t you recognize how astronomically improbable that is?

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