Answer to Barry Part 1 (and, inadvertently, 2)

Barry seems to have noticed TSZ again, and so I will take this opportunity of inviting him over here, where he can post freely, and will not be banned unless he posts porn or malware or outs someone, which I expect he can manage not to do.

And he responds to my post, Lawyers and Scientists.  He does so in two parts, so I will devote two posts to them.  Here is my response to his first part.  Barry writes:

PART 1

First Liddle writes that I have

. . . confused the assumption of common descent with the conclusion of common descent, and thus detected circular reasoning where there is none.

Where did I do such a thing?  Boiling that paragraph down I made the following claims:

  1. Common descent is not necessarily false.
  1. But Cladistics does not establish common descent one way or the other.
  1. Instead, cladograms are constructed ASSUMING common descent.
  1. It is circular reasoning to conclude that a technique establishes that which it assumes in the first place.
  1. Therefore, anyone who says that cladistics establishes the fact of common descent has used faulty reasoning and is mistaken.
  1. There are in fact people who make that mistake.

To establish beyond doubt point 6, Glen Davidson kindly jumps into Liddle’s own combox with this:

Barry:  “This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.”

Glen:  “Of course it does. What a ridiculously ignorant dweeb.”

All six assertions seem to me to be on solid ground.  Not only are they true, they are not even controversial.  But for Liddle’s charge to be correct, at least one of the points I made must be false.  OK Liddle, which of the six totally non-controversial points I have made do you disagree with?  If the answer is “none,” then the only gracious thing to do is to withdraw your claim.

The short answer is that I disagree with 2-6, for the reasons I gave in my first post: the answer lies in null hypothesis testing.  Far from “assuming a tree”, both linear correlations and tree distributions are tested by FITTING a slope/tree, and testing whether the best fit is a better fit than would be expected under the NULL of no linear relationship/no underlying tree structure.  If, having fitted the slope/tree, the fit is no better than would be expected under the null of no linear relationship/no underlying nested hierarchy, then you RETAIN THE NULL.  If it is  better, i.e. if a fit as good as that observed is UNLIKELY under the null, you reject the null and consider your hypothesis (linear fit; common descent pattern) supported. Of course there could reasons other than common descent that could explain the tree – but the tree can be established as an OBSERVATION to be EXPLAINED.  Which Linnaeus did before Darwin.  And it was that clear tree that Darwin sought to explain by, firstly, Common Descent, and, secondly, by a mechanism that would explain adaptive change-over-time.

If Barry cannot understand that testing a NULL HYPOTHESIS is the OPPOSITE of assuming that your model is true, then perhaps he could shoot an email to the former owner of his site.

It is of course true that null hypothesis testing is counter-intuitive and doesn’t do what many of its practitioners think it does, but it’s still an excellent workhorse, and what’s more, is the beating heart of ID’s very own eleP(T|H)ant.

[My response to the second part will have to wait – I have some null hypotheses to test first….]

ETA: Looks like this response deals with Pt II at as well.

180 thoughts on “Answer to Barry Part 1 (and, inadvertently, 2)

  1. OMagain: Demonstrate a better way then. Or do you only point out things you think are wrong without suggesting alternatives?

    You already know what my alternative is. It involves platonic forms and a 4 dimensional grid.

    My suggestion that we don’t worry ourselves so much on the hypothetical origin of species and instead look at their relative morphology and relationships to other species and the universe as a whole.

    that is just me

    peace

  2. John Harshman:
    fifthmonarchyman,
    Do you in fact know anything whatsoever about phylogenetic analysis? You seem to be imagining a scenario to fit your fantasies.

    He does not. This discussion with him is too superficial and in generalities. You will have to go much more in-depth and explain what it is you actually do, why you do that, and then point out in simple, elaborate step by step fashion how the “tree is probably a warranted rational conclusion”.

    What are all the key inferences, why are they made, why does the conclusion follow? You are talking with someone who knows nothing of the subject, so words like “bootstrap”, “nodes”, “branch length”, etc etc is just esoteric technobabble to him.

  3. OMagain: You’ve somehow forgotten to demonstrate how you know that species are a distinct concept in the mind of god.

    Premise 1) I can conceive of distinct species
    Premise 2) God is smarter than me
    Conclusion) God can conceive of distinct species.

    this concludes the demonstration

    peace

  4. fifthmonarchyman: You already know what my alternative is. It involves platonic forms and a 4 dimensional grid.

    But what’s that an alternative to? It can’t be an alternative to phylogenetic analysis as phylogenetic analysis actually generates new information! Whereas you have been unable to generate a single data point from your “scheme” at all.

    So if your scheme is an alternative to phylogenetic analysis then please analyse something and demonstrate that your alternative is actually useful!

    Or make up an excuse why you can’t and continue to think as you are, it’s really up to you.

  5. fifth,

    How exactly? Be specific as to how science can prove a negative

    This sort of thing is why people despair of having an intelligent conversation with you.

    Science can’t “prove” negatives because it can’t “prove” anything, but it certainly gives us reasons to reject certain claims.

    Scientifically literate people believe that n-rays don’t exist. They do so on scientific grounds, and they are justified in their rejection.

    Do you disagree?

  6. Neil Rickert: I agree with that. However, inductionism seems to be deeply ingrained in western culture.

    Ingrained in western culture does not equal “true” as I’m sure you would agree.

    Lots of what we think are obvious self-evident truths are nothing but cultural castles of sand.

    peace

  7. fifthmonarchyman:
    OMagain,

    Speaking of patterns and essences
    Any progress on the tool/Game?

    It’s whole point is to investigate whether patterns we see are actual or just imposed on the data in an ad-hock manner. It or something like it might work with the data we are talking about here.

    peace

    The patterns are in the data.

    If you are looking for imposition, then you are looking in the wrong place.

    The world comes to us without data. What we impose, are our methods of getting useful data. And that implicitly imposes some structure on the data. If we use structured methods of getting data, then the data will reflect that structuring.

  8. Neil Rickert: What we impose, are our methods of getting useful data. And that implicitly imposes some structure on the data.

    Now that is an interesting comment!!!

    Have I told you that you and I could have some fun conversations on the front porch with a beverage?

    peace

  9. fifthmonarchyman: You already know what my alternative is. It involves platonic forms and a 4 dimensional grid.

    If you want your alternative to be used, then you must provide a compelling reason for people to swap over to it.

    What’s the compelling reason?

  10. fifthmonarchyman: Ingrained in western culture does not equal “true” as I’m sure you would agree.

    The idea of ultimate truth is also ingrained in western Culture, though perhaps not as strongly ingrained as inductionism.

    Lots of what we think are obvious self-evident truths are nothing but cultural castles of sand.

    I suggest you apply that idea to your own “self-evident truths” about religion and revelation.

  11. OMagain: If you want your alternative to be used, then you must provide a compelling reason for people to swap over to it.

    I really don’t care if my alternative is used. It’s no skin off my nose either way.

    To each his own

    What I’m bugged about is when people act as if their approach is the only possible one without providing a compelling reason for doing so.

    What is the compelling reason?

    peace

  12. Neil Rickert: The idea of ultimate truth is also ingrained in western Culture

    Ingrained in western culture does not equal true but it does not equal “not true” either 😉

    Neil Rickert: except that I think your religious zeal might get in the way.

    It’s possible but I expect that we could learn to negotiate the pitfalls of colliding mutually exclusive worldviews with a little patience and mutual understanding.

    happy Thanksgiving

    peace

  13. keiths: Scientifically literate people believe that n-rays don’t exist. They do so on scientific grounds, and they are justified in their rejection.

    Do you disagree?

    yes

    peace

  14. fifth,

    We already covered that. I wrote:

    Science can’t “prove” negatives because it can’t “prove” anything, but it certainly gives us reasons to reject certain claims.

    Now you are in the ridiculous position of saying that we are not scientifically justified in rejecting the existence of n-rays.

  15. Let’s say that I wanted to understand the timing and patterns of genetic variation associated with the recent Ebola outbreak. I could use phylogenies to date the outbreak and examine patterns of nucleotide or amino acid substitution along branches of those phylogenies to learn about how the virus is evolving (as Gire and colleagues did here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431643/).

    How would utilizing “platonic forms and a 4 dimensional grid” improve upon this method?

  16. keiths: Now you are in the ridiculous position of saying that we are not scientifically justified in rejecting the existence of n-rays.

    All we are justified in saying scientifically is that n-rays have not been empirically demonstrated to exist. That is a far cry from saying emphatically that they don’t exist.

    Your apparent scientism keeps you from seeing this obvious fact.

    For you “has not been empirically demonstrated to exist” is equivalent to “does not exist”.

    They are not remotely the same thing

    peace

  17. I am a bit jealous. Elizabeth has been reinstated at UD but I haven’t. 🙁 Maybe I should just create a new persona like Joe did. But then I’d be compromising my moral standards. Does that matter as far as UD is concerned? Such ethical questions. I need another glass of wine.

  18. Alan, I noticed that you didn’t respond to my comments on nested hierarchies. Does that mean you now agree with me? Or is it that you just don’t have any rebuttal?

  19. Jerad: True, but the emotional angst is hard to bare . . . or do I mean bear?

    You don’t have anything of substance to add so why even bother posting at UD?

  20. Frankie: You don’t have anything of substance to add so why even bother posting at UD?

    This is an open forum for discussion of a wide range of issues. Everyone who wishes to can comment here, provided they are happy to abide by the not-very-onerous rules.

  21. Alan Fox: This is an open forum for discussion of a wide range of issues. Everyone who wishes to can comment here, provided they are happy to abide by the not-very-onerous rules.

    Non-sequitur

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