Intelligent Design

Liddle Inadvertently Establishes That Which She Attempts to Refute

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Over at The Skeptical Zone Elizabeth Liddle quotes me regarding the circular reasoning that would be necessary to suppose that cladistics establishes common descent:

It does not take a genius to know that cladistic techniques do not establish common descent; rather they assume it.  But I bet if one asked, 9 out of 10 materialist evolutionists, even the trained scientists among them, would tell you that cladistics is powerful evidence for common descent.  As Johnson argues, a lawyer’s training may help him understand when faulty arguments are being made, sometimes even better than those with a far superior grasp of the technical aspects of the field.  This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.

In response to this Liddle calls me out and charges me with making two errors, which I will address in turn:

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.

PART 2

Secondly, Liddle says I have

. . . confused the process of fitting a model with the broader concept of a hypothesised model . . .

The analogy here with cladistics is: choosing to fit a tree model does not entail the assumption that a tree model will fit.  What is tested is the null of “no tree” . . .

So my second point is that when a palaeontologist fits a tree model to her data, she is a) testing the null hypothesis that the data are not distributed as a tree . . .

I take it that Liddle’s point is that cladistics does not always assume common descent but also “tests” the assumption of common descent.

This assertion is risible and betrays a profound misunderstanding of how cladistics works.  As a matter of simple logic, a technique cannot test that which it assumes to be true in the first place.  The assumption of common descent in cladistics is pervasive from beginning to end.

But don’t take my word for it.  This is what that bastion of conservatism and design theory the University of California, Berkeley Museum of Paleontology says in its Journey into Phylogenetic Systematics:

There are three basic assumptions in cladistics:

  1. Any group of organisms are related by descent from a common ancestor.
  2. There is a bifurcating pattern of cladogenesis.
  3. Change in characteristics occurs in lineages over time.

The first assumption is a general assumption made for all evolutionary biology. It essentially means that life arose on earth only once, and therefore all organisms are related in some way or other. Because of this, we can take any collection of organisms and determine a meaningful pattern of relationships, provided we have the right kind of information. Again, the assumption states that all the diversity of life on earth has been produced through the reproduction of existing organisms.

The same site says that cladistics has three uses:  (1) it is a system of classification; (2) it helps make predictions about properties of organisms based on the assumption of common descent; and (3) it helps in the testing evolutionary mechanisms.

I invite readers to go to that site and read it in full.  It says nothing about Liddle’s proposed fourth use of cladistics – testing (as opposed to assuming) common descent to begin with.

For goodness sake, Liddle, even uber-Darwinist Nick Matzke agrees that cladistics cannot establish common descent.  He wrote:

. . . phylogenetic methods as they exist now [cannot] rigorously detect . . . direct ancestry, and, crucially, . . .  this is neither a significant flaw, nor any sort of challenge to common ancestry, nor any sort of evidence against evolution.

Certainly Nick is right* that cladistics’ inability to establish common ancestry does not mean that common ancestry is necessarily false.  But that is exactly what I said in the part Liddle quoted:  “This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.”

Liddle is simply wrong when she says that cladistics tests, as opposed to assumes, the claim of common ancestry.

Liddle knows this as well as anyone I suspect, and explains why in the very same post she walks back on her initial claim when she writes:

Of course palaeontologists aren’t seriously testing the null hypothesis that the data are distributed as a tree – we know, from countless cladistics studies that they are, and it isn’t even disputed by anyone.

Again, as Matzke says, all of this does not necessarily mean that common descent is false.  I made no assertion regarding that matter one way or the other.  It does not mean that cladistics cannot simultaneously assume and test common descent.  Simple logic.

So Liddle’s attempt to show that a lowly lawyer has nothing useful to say has blown up in her face.  Far from establishing that, by using faulty logic and reasoning – things that as a lawyer I am trained to detect – she has actually established that which she set out to refute.

 

 

 

_____________

*Bovina Sancta!  Can I actually be agreeing with Nick about something?  I suppose it is true that even a blind squirrel finds and acorn now and then.

170 Replies to “Liddle Inadvertently Establishes That Which She Attempts to Refute

  1. 1
    bFast says:

    Barry, may I disagree with you that “Cladistics does not establish common descent one way or the other.” I think that cladistics is necessary for common descent to be true.

    However, the inverse is not necessarily true. We clearly see a strong cladistic nature to modern technology, yet we know that modern technology is not a product of classic common descent.

  2. 2
    Barry Arrington says:

    bFast

    Barry, may I disagree with you that “Cladistics does not establish common descent one way or the other.”

    Yes, just as soon as you demonstrate how it can demonstrate that which it assumes in the first place.

    I think that cladistics is necessary for common descent to be true.

    If one assumes comment descent is true, cladistics follows. My point is that it does not work the other way around. If one assumes cladistics is true, common descent does not necessarily follow.

  3. 3
    Zachriel says:

    Barry Arrington: As a matter of simple logic, a technique cannot test that which it assumes to be true in the first place.

    All hypothesis-testing depends on making the assumption of what is to be tested.

    Analytics can provide statistical confidence in a hypothesized tree. A common method is with Monte Carlo tests. In other words, it can quantify the “tree-ness” of the data.

    bFast: We clearly see a strong cladistic nature to modern technology, yet we know that modern technology is not a product of classic common descent.

    Actually, human artifacts generally fail the test, as they can be arranged into many different, equally rational trees.

  4. 4
    Barry Arrington says:

    Z

    In other words, it can quantify the “tree-ness” of the data.

    Yes, it certainly can if it assumes the data should be modeled by a tree to begin with. Why is this so hard to understand? You are making the same error Liddle made.

  5. 5
    Zachriel says:

    Barry Arrington: Yes, it certainly can if it assumes the data should be modeled by a tree to begin with.

    Cladistics assumes the data forms a tree, and determines the best-fit. However, it can then be determined how closely the data conforms to the tree structure, such as whether branches can be rearranged without affecting the degree of fit. This provides a statistical measure of whether the tree structure is strongly or weakly supported.

    There’s little doubt that the tree structure is strongly supported for most taxa.

  6. 6
    Barry Arrington says:

    Z

    Cladistics assumes the data forms a tree . . .

    Exactly. Therefore, it cannot establish that the data forms a tree. Do you understand now?

  7. 7
    Mung says:

    Does cladistics test the null or the non null?

  8. 8
    Zachriel says:

    Barry Arrington: Therefore, it cannot establish that the data forms a tree.

    Try to respond to the points raised.

    1. We can use statistics (e.g. Monte Carlo) to determine whether the proposed tree is strongly supported or weakly supported.
    2. The tree-structure is strongly supported across most taxa.

  9. 9
    Mung says:

    Zachriel: All hypothesis-testing depends on making the assumption of what is to be tested.

    So?

  10. 10
    Mung says:

    Zachriel: Actually, human artifacts generally fail the test, as they can be arranged into many different, equally rational trees.

    What does an irrational tree look like?

  11. 11
    Zachriel says:

    Mung: So?

    Hypothesis-testing is not circular reasoning, even though it assumes what it is trying to show. That’s because the statement is evaluated according to its fit to the evidence.

    H => E
    E
    therefore H is supported

    H => E
    ~E
    therefore H is falsified

    Nor is it a fallacy of affirming the consequent, as H is not claimed to be necessarily true simply because it is supported.

  12. 12
    Barry Arrington says:

    Zach

    Two statements are on the table:

    1. Yours: “Cladistics assumes the data form a tree.”

    2. Mine: “Therefore, it cannot establish that the data form a tree”

    I asked you whether statement 2 follows from statement 1, and in bad faith you tried to dodge the question. That is what you always do when you’re stuck. Not this time. You are in moderation. You will not be released from moderation until you answer the question. If this means you never post at UD again, I can live with that.

  13. 13
    Zachriel says:

    Mung: What does an irrational tree look like?

    Artifacts generally form many different trees with similar degrees of fit.

  14. 14
    Zachriel says:

    Barry Arrington: 1. Yours: “Cladistics assumes the data form a tree.”

    2. Mine: “Therefore, it cannot establish that the data form a tree”

    Hypothesis: the Earth spins on its axis
    Test: retardation of the pendulum.

    Hypothesis: data forms a tree structure.
    Test: statistical tests to determine how well the data conforms to a tree structure.

  15. 15
    wookieeb says:

    Z: Cladistics assumes the data forms a tree, and determines the best-fit.

    We can use statistics (e.g. Monte Carlo) to determine whether the proposed tree is strongly supported or weakly supported.

    Yes, cladistics assumes “a tree”. There may be multiple trees modeled, with some statistically more strongly supported vs other trees. But no matter what, in the end, there will always be “a tree”.

    Cladistics does not assume for, nor even allows for a ‘not-tree’.

    So because cladistics assumes a tree, it can never be used to determine whether there really is a tree or not-tree.

  16. 16
    Zachriel says:

    wookieeb: Cladistics does not assume for, nor even allows for a ‘not-tree’.

    Yes, but it turns out that the tree structure is strongly supported across many taxa.

  17. 17
    Barry Arrington says:

    wookieeb,

    Your conclusion is glaringly obvious. It seems to have escaped Liddle and Zach.

    Interestingly, even Matzke admits that the process cannot establish what it assumes.

    All of this leads us away from the actual point to ruminations about the psychology of people like Zach whose ideological agenda makes him literally blind to simple and obvious truths. It is very sad.

  18. 18
    REW says:

    Barry,

    The assumption behind cladistics is that because of common descent, if we use a certain procedure to organize data we’ll get a tree-like pattern as a result. The important point is that the procedure does not itself create a tree-like pattern necessarily. When one performs the procedure on a set of data one might or might not get the tree-like pattern. The fact that biologists overwhelmingly get the tree-like pattern is evidence for common descent.
    I think bFast might be correct that if you took some technological objects you might sometimes get trees but then the next important step would be to analyze why you’d get trees in this case. There are many other cases where I’m pretty sure you wouldn’t but again its still doable in principle. I’m surprised IDers don’t work on this. If you could rigorously show that if you take a set of objects that clearly are unrelated and apply cladistics methods you always get trees ( as you imply) that would make a great talking point against biologists.
    I’m not sure what you mean when you say: “Nick Matzke agrees that cladistics cannot establish common descent.”
    He says clearly the cladistics strongly supports common descent. Its just unable to show direct ancestry. So we can never be sure if some fossil organism is the direct ancestor of any other organism or just a relative of its ancestor.
    I guess you could say that cladistics doesn’t provide direct evidence of common ancestry. For that you’d have to watch living things for tens of millions of years. But it is exactly what you’d expect if things are evolving by descent with modification. If you can find a better explanation for the pattern in the data, again as bFast suggested, you should write it up in detail.

  19. 19
    Jack Jones says:

    “All of this leads us away from the actual point to ruminations about the psychology of people like Zach whose ideological agenda makes him literally blind to simple and obvious truths. It is very sad.”

    It is pathetic really Mr Arrington but it shows we are dealing with a person guided by emotion and not reason when it comes to zach and also those evolutionists that would continue on like him.

  20. 20
    wd400 says:

    The lastt definition of specified complexity offered by dembski includes the term P(T|H), which is the probability of some evolutionary event “T” assuming a chance hypothesis “H” was responsible for generating it.

    Do we now conclude that specified complexity can’t tell us about chance hypotheses one way or another (since the hypothesis has to be assumed to calculate CSI)? Or are you simply saying statistical methods won’t prove something absolutely beyond doubt (which I don’t anyone will disagree with)?

  21. 21
    Virgil Cain says:

    REW- We can make a tree out of transportation (Denton “Evolution: A Theory in Crisis” 1985) and Linnaean taxonomy produces a tree that Linnaeus said was expected of a Common Design. The US Army is another tree that is we formed without common descent.

  22. 22
    Barry Arrington says:

    REW:

    The assumption behind cladistics is that because of common descent, if we use a certain procedure to organize data we’ll get a tree-like pattern as a result.

    Yes, that is what I have been saying.

    The important point is that the procedure does not itself create a tree-like pattern necessarily.

    Of course it does. That is the whole point of it.

    The fact that biologists overwhelmingly get the tree-like pattern is evidence for common descent.

    No. It demonstrates that when one makes an assumption and then interprets all data in light of that assumption, one will overwhelmingly find that that the data conform to the assumption.

    Berlinski says this:

    [P]hylogenetic methods as they exist now,” [Matzke] writes, “can only rigorously detect sister-group relationships, not direct ancestry, and, crucially, … this is neither a significant flaw, nor any sort of challenge to common ancestry, nor any sort of evidence against evolution.” But there can be no sisters without parents, and if cladistic analysis cannot detect their now mythical ancestors, it is hard to see what is obtained by calling them sisters. No challenge to common ancestry? Fine. But no support for common ancestry either. Questions of ancestry go beyond every cladistic system of classification, no matter the character states. . . .

    The relationship between cladistics and Darwin’s theory of evolution is thus one of independent origin but convergent confusion. “Phylogenetic systematics,” the entomologist Michael Schmitt remarks, “relies on the theory of evolution.” To the extent that the theory of evolution relies on phylogenetic systematics, the disciplines resemble two biologists dropped from a great height and clutching at one another in mid-air.

    Tight fit, major fail.

    Again, this is so staggeringly obvious that I am astounded that we are having this conversation.

    Do you disagree with the following statements of logic:

    1. X assumes A.
    2. Therefore, X cannot establish A as a fact.

  23. 23
    wd400 says:

    I think you’ve also misconstrued Nick M’s comment.

    My reading of the linked article has Nick saying you can’t test the hypothesis “Fossil A is direct ancestor of Living Species B”. That’s true enough. But phylogenetic methods include ancestral traits, it’s just we can’t assign taxa to the nodes of trees (currently).

  24. 24
    Barry Arrington says:

    wd400

    “Or are you simply saying statistical methods won’t prove something absolutely beyond doubt (which I don’t anyone will disagree with)?”

    I am saying that as a matter of logic, nothing can demonstrate that which it assumes in the first place.

  25. 25
    Virgil Cain says:

    Cladistics isn’t a test for Common Descent anymore than it is a test for a Common Design.

    Cladistics is a method of categorizing organisms based on shared characteristics. Each clade allegedly consists of a common ancestor and all of its descendents. However we can also say that each clade consists of a common design and all its descendent variations. For example, all cars are descended from the originally created cars, the designs that survived and were reproduced- descended by design. All computers are descended, by design, from the originally created computers. The closer the ancestry the more similarities.

    And so it would go for living organisms. So there you have it, per Elizabeth, Common Design is tested and verified.

  26. 26
    Barry Arrington says:

    wd400,

    Read the Berlinski quote.

    Nick is saying we can detect “sister” relationships even though we cannot detect “parent” relationships, which, of course, is incoherent.

  27. 27
    Barry Arrington says:

    Here’s another one of those invisible gorillas.

    Every Darwinist who has commented so far has ignored the UC Berkeley statements.

    Surely if cladistics was designed to test common descent (as opposed to assuming it), UC Berkeley would have mentioned that. It did not. That 500 pound gorilla is very conspicuous.

    Do any of the Darwinist commenters dare look at it and try to explain it away?

  28. 28
    Zachriel says:

    Barry Arrington: 1. X assumes A.
    2. Therefore, X cannot establish A as a fact.

    Hypothesis-testing is not circular reasoning, even though it assumes what it is trying to show. That’s because the statement is evaluated according to its fit to the evidence.

    H => E
    E
    therefore H is supported

    H => E
    ~E
    therefore H is falsified

    Nor is it a fallacy of affirming the consequent, as H is not claimed to be necessarily true simply because it is supported.

    Hypothesis: the Earth spins on its axis
    Test: If the Earth spins on its axis (assumption) then the pendulum will be retarded.

    Hypothesis: data forms a tree structure.
    Test: If the data forms a tree structure, then statistical tests will show strong support for a tree structure.

    (The latter doesn’t even require a hypothesis of branching descent. We’re just looking at data to see if it forms a tree structure.)

  29. 29
    wd400 says:

    Nick is saying we can detect “sister” relationships even though we cannot detect “parent” relationships, which, of course, is incoherent.

    He’s saying you can calculate a likelihood that two species are sister, but not a likelihood that one species is parent to another. You’ll have to tell me why you think that’s “incoherent”

  30. 30
    Barry Arrington says:

    wd400
    You’ll have to tell me why you think that’s “incoherent”

    Read Berlinski’s takedown. Tell me why you think he is wrong.

  31. 31
    Barry Arrington says:

    Zach, you have descended into your “endless repeat” mode. Desist. Unless you have something to add, no need to say what you’ve already said (twice now), and if you do your time will have been wasted, because your comments that do nothing but repeat your prior comments will be deleted.

  32. 32
    wd400 says:

    Berlinksi makes no argument to support his conclusion.He correctly states that there are not sisters without parents, but then claims inferring sister-relationshps (and therefore ancestors) is of no worth if you can’t also assign specific species to ancestor -> descendant relationships without explaining why he thinks it’s the case.

  33. 33
    Zachriel says:

    Barry Arrington: It is tempting precisely because it invites the taxonomist to undertake an inference from the premise that B is between A and C to the conclusion that B is somehow a descendent of A, an ancestor of C.

    Can you point out the error?

    Barry Arrington: you have descended into your “endless repeat” mode.

    And you have descended into your “endless ignoring” of the point raised: The use of the hypothesis as the assumption of what is to be supported or falsified (schematic and examples shown @28).

  34. 34
    Gordon Davisson says:

    [Now that I’ve written this, I see that Zachriel made essentially the same point @28. Oh, well, posting anyway]

    Barry, you’re mistaking abductive inference for deductive inference. Science uses abductive inference as a primary method for testing and supporting hypotheses, but if you try to read it as deductive inference it’ll sound like nonsense. Here’s a simple example:

    Deductive inference: if X is a duck, then it’ll walk, swim, quack, etc like a duck.

    Abductive inference: if X walks, swims, quacks, etc like a duck, then it’s probably a duck or something similar enough that we can reasonably treat it as a duck (until/unless we find a better explanation).

    If you try to treat the abductive inference as a deductive inference (something like “if X walks, swims, quacks, etc like a duck, then it’s a duck”), and put that together with the valid deductive inference, you’ll get a logical circle. But that’s not what’s going on here.

    Before I get to what is going on, let me give you a less trivial (and actually historically correct) example:

    Deductive inference: if Newton’s theory of gravity is correct, then planets will follow elliptical orbits (with the sun at one focus) and all dropped objects will fall at the same rate independent of their weight.

    Abductive inference: if planets follow elliptical orbits (with the sun at one focus) and all dropped objects fall at the same rate, then Newton’s theory of gravitation is probably correct or at least close enough enough that we can reasonably treat it as true (until/unless we find a better explanation).

    Note that abductive inference does not give absolute certainty, and experience shows that the inferred explanation is generally close to, but not exactly, correct. Newton’s theory of gravity is a perfect example: it’s very close under most circumstances, but not exactly right. And BTW its replacement, general relativity, is also probably not exactly right, but it’s even closer.

    Now, there are a number of variations on this, as well as different ways of understanding it (successful prediction/retrodiction/explanation, Baysian inference, etc), but whatever the details this you’ll find sort of inference all over science.

    For example, the recent discovery of the Higgs boson: if the Higgs exists, we should get excess events at a certain energy level from the Atlas experiment; we got excess events from the Atlas at about 125GeV, so the Higgs (or something similar to it) is probably real.

    Barry, do you think the reasoning above is circular?

    Ok, let’s try it with cladistics and common ancestry with bifurcating lineages:

    Deductive inference: if living organisms are related by common ancestry with bifurcating lineages, then cladistics will be a useful way of organizing living organisms.

    Abductive inference: if cladistics is a useful way of organizing living organisms, then living organisms are probably related by common ancestry with bifurcating lineages or something similar.

    Now, since cladistics is a useful way of organizing living organisms, we can make the inference that common ancestry with bifurcating lineages is probably approximately true.

    Actually, as with Newtonian gravity, we know that it’s not exactly right, because there are all sorts of complications going on as well: lineages sometimes merge (though mostly closely related ones, so it doesn’t mess up the overall tree much), there are a few places where highly diverged branches have merged (via endosymbiosis), there might be a mess of cross-connected lineages at the root of the tree, etc. But as with Newtonian gravity, this doesn’t change the fact that there’s strong (abductive) evdence that common ancestry is at least a very good approximation.

    BTW, for those who are pointing out that you can force a cladistic organization on anything: that’s true, but the result won’t generally do a good job of representing the similarities and differences between the categorized objects. You disagree? Try it with cars. You’ll find that there’s no way to get all of the cars with automatic transmissions together without having different engine types, body styles, models and manufacturers, etc splattered all over the tree. Get things organized by model and/or manufacturer, and the transmission types, engines, body styles, etc are now splattered all over. Cladistic categorization works for organisms in a way that it doesn’t for most things. The tests Zachriel is talking about are a more formal way of checking this, but really all you have to do is look at a range of organisms; you don’t really need formal tests, the fit is obvious.

  35. 35
    Virgil Cain says:

    Cladistics assumes the data forms a tree,

    Which is a good thing as cladistics is about constructing trees.

    Well done, Zachriel, the master of minutiae; the beyotch of bloviation; the epitome of jackassery.

  36. 36
    Barry Arrington says:

    wd400,

    Darwinian expert in Cladistics Michael Schmitt literally wrote the book on the subject. He says, as Berlinski notes,

    Phylogenetic systematics relies on the theory of evolution, which does not lead into circularity, since phylogenetic systematics does not claim to prove or to explain evolution whatsoever.

    Do you agree with him? I do.

    Further, the ONLY way the project can avoid circularity is in exactly the way Dr. Schmitt says. Again, this is glaringly obvious. Logic and the leading DARWINIAN experts say the same thing. Why does this obvious conclusion get so much push back? That is an interesting question.

  37. 37
    Virgil Cain says:

    Gordon Davisson:

    Now, since cladistics is a useful way of organizing living organisms, we can make the inference that common ancestry with bifurcating lineages is probably approximately true.

    In what way is it useful?

  38. 38
    Barry Arrington says:

    Gordon Davisson,

    I ask you the same question I asked wd400 in 36.

  39. 39
    Zachriel says:

    Gordon Davisson: [Now that I’ve written this, I see that Zachriel made essentially the same point @28. Oh, well, posting anyway]

    You made the point better. Also, sometimes explaining something in other words may make it more understandable to some readers.

  40. 40
    Barry Arrington says:

    BTW Gordon,

    All ID proponents understand what an abductive inference is. Because design inferences are abductive in nature.

    If all you are saying is: “We have assumed common descent and we can often arrange the data in a way that is consistent with that assumption,” then who could disagree with that. When I said “establishes” in my original post it was clear I was talking about just that: establishes as a matter of fact.

    If you agree that cladistics does not establish common descent as a matter of fact, then we are in agreement (albeit apparently violent agreement). Now go tell Liddle.

  41. 41
    wd400 says:

    Just so we can keep track of the arguments you left behind, can you .

    (1) Confrim that your problems with assumptions apply to CSI
    (2) Let us know why inferring sister-relationships but no parent->descendant relationships is incoherent.

    With that, I obviously disagree with Schmitt’s comment as it is presented. I should not that it is written about phylogenetic systematics which is a technical term for the school of taxonomy that was the centre controversy at the time the article was written. Phylogenetic systematics has largely been replaced by statistical phylogenetics in fields other than taxonomy (thanks largely to some-time UD commenter Joe Felsenstein). It’s possible Schmitt’s comments are more limited when read in context (I don’t have acess to that journal).

    Finally.

    When I said “establishes” in my original post it was clear I was talking about just that: establishes as a matter of fact.

    OK, but that’s a tiny and non-controversial claim.What facts are established in this sense in science? And by what means where they established?

  42. 42
    Gordon Davisson says:

    Barry: I haven’t read Michael Schmitt’s article (nor am I any sort of expert in the field), but I think he’s making the distinction between categorization methods that assume evolution and try to fit evolutionary history vs those that simply look at characters and categorize based on them. There is a potential circularity where making assumptions about evolution leads to a result that matches the assumptions; that match cannot be used to support the assumptions.

    But there’s a very similar non-circular version: make assumptions about evolution, derive resulting categorization from those assumption, find the result matches actual data; that match can be used to support the original assumptions. The key is checking against something external to the assumptions.

    BTW, if I understand the boundaries he’s defining properly, I agree completely with Michael Schmitt: phylogenetic systematics itself does not test evolution. But that in no way shape or form means that phylogenetic systematics cannot be used as part of a test of evolution.

  43. 43
    Virgil Cain says:

    (1) Confrim that your problems with assumptions apply to CSI

    What assumptions are made with respect to CSI?

    (2) Let us know why inferring sister-relationships but no parent->descendant relationships is incoherent.

    How can you tell they are sisters without knowing the parent(s)?

  44. 44
    Virgil Cain says:

    Common ancestry needs a mechanism that can account for all of the physiological and morphological changes required. There isn’t any data that supports the claim that changes to genomes can produce those required changes. And if descent with modification requires more than just modifying genomes it doesn’t have a mechanism.

  45. 45
    wd400 says:

    (1) P(T|H) is part of CSI, that’s probability of “T” assuming the relevant chance hypothesis generated it.

    (2) If you sequenced the DNA of two women and find they they share the same allele in ~50% of sites that vary widely in the human population. Would you conclude it’s more probable that they are sisters than two people plucked at random from a population? Companies like 23andMe do precisely these calculations, btw.

  46. 46
    bornagain says:

    What convinced me that cladistics was, as far as it is used by Darwinists, a bogus Darwinian shell game was having Dr. Literature Bluff himself,,,

    A short history of Matzke’s literature bluffing – Nov. 2015
    http://www.uncommondescent.com.....ent-589458

    ,,,Nick Matzke, try to use it as proof against the Cambrian explosion when Meyer’s book ‘Darwin’s Doubt’ came out.

    Dr. Meyer addressed Matzke’s imaginative use of cladistics here

    Cladistics Made Easy: Why an Arcane Field of Study Fails to Upset Steve Meyer’s Argument for Intelligent Design

    Stephen Meyer – Responding to Critics: Matzke Part 1 – video
    https://www.youtube.com/watch?v=jY2B76JbMQ4

    Stephen Meyer – Responding to Critics: Matzke Part 2 – video
    https://www.youtube.com/watch?v=lZWw18b3nHo

    Responding to Critics: Matzke Part 3 – video
    https://www.youtube.com/watch?v=77XappzJh1k

    Luskin unpacks ENV’s responses to critic Nick Matzke, exploring the classification of organisms, cladistics, and the origin of arthropods.

    podcast: “Debating Darwin’s Doubt: Casey Luskin on Classification of Organisms”
    http://intelligentdesign.podom.....1_23-07_00

    A One-Man Clade – David Berlinski – July 18, 2013
    Excerpt: The relationship between cladistics and Darwin’s theory of evolution is thus one of independent origin but convergent confusion. “Phylogenetic systematics,” the entomologist Michael Schmitt remarks, “relies on the theory of evolution.” To the extent that the theory of evolution relies on phylogenetic systematics, the disciplines resemble two biologists dropped from a great height and clutching at one another in mid-air.

    Tight fit, major fail.7

    No wonder that Schmidt is eager to affirm that “phylogenetics does not claim to prove or explain evolution whatsoever.”8 If this is so, a skeptic might be excused for asking what it does prove or might explain?
    http://www.evolutionnews.org/2.....74601.html

    Dr. Behe has stated in several of his talks that,,,

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe – 29:24 mark of following video
    http://www.youtube.com/watch?f.....fM#t=1762s

    And if anything was ever ripe for abuse by the ‘undisciplined imagination’ of Darwinists it is certainly cladistics.

    Basically all someone has to do in order to infer a relationship, no matter how remote, is draw a line on a cladistic diagram.
    i.e. The line on the sheet of paper is basically just subjectively imagined from a relationship that may or may not exist and has no real empirical connection to the real world.

    Cladistics, as it is (ab)used by Darwinists is certainly not empirical science.

    Moreover, when we get down to empirical science, to see if such radical transitions in form envisioned in universal common descent are even possible, that is where Darwinian imagination meets reality, and where Darwinian ‘just so stories’ are shown to be completely inadequate for what we can expect from unguided material processes. (Behe, Axe, Gauger, etc.. etc..)

    The fact of the matter is that Darwinian evolution has ZERO real time empirical evidence that unguided material processes can create ANY non-trivial information, and that Darwinian evolution is absolutely dependent on imagination, such as is seen in cladistic diagrams, in order to seem plausible.

    Basically, Darwinian evolution is reliant on smoke and mirrors deception, not unlike the sleight of hand that a magician uses, to try to convince the gullible that unguided material processes have basically pulled off the miraculous and created all life on earth in all its stunning diversity and wondrous complexity.

    EVOLUTIONARY JUST-SO STORIES
    Excerpt: ,,,The term “just-so story” was popularized by Rudyard Kipling’s 1902 book by that title which contained fictional stories for children. Kipling says the camel got his hump as a punishment for refusing to work, the leopard’s spots were painted on him by an Ethiopian, and the kangaroo got its powerful hind legs after being chased all day by a dingo.
    Kipling’s just-so stories are as scientific as the Darwinian accounts of how the amoeba became a man.
    Lacking real scientific evidence for their theory, evolutionists have used the just-so story to great effect. Backed by impressive scientific credentials, the Darwinian just-so story has the aura of respectability.
    Biologist Michael Behe observes:
    “Some evolutionary biologists–like Richard Dawkins–have fertile imaginations. Given a starting point, they almost always can spin a story to get to any biological structure you wish” (Darwin’s Black Box).,,,
    http://www.wayoflife.org/datab.....ories.html

    Darwinian ‘science’ in a nutshell:
    Jonathan Wells on pop science boilerplate – April 20, 2015
    Excerpt: Based on my reading of thousands of Peer-Reviewed Articles in the professional literature, I’ve distilled (the) template for writing scientific articles that deal with evolution:
    1. (Presuppose that) Darwinian evolution is a fact.
    2. We used [technique(s)] to study [feature(s)] in [name of species], and we unexpectedly found [results inconsistent with Darwinian evolution].
    3. We propose [clever speculations], which might explain why the results appear to conflict with evolutionary theory.
    4. We conclude that Darwinian evolution is a fact.
    http://www.uncommondescent.com.....ilerplate/

  47. 47
    Virgil Cain says:

    (1) P(T|H) is part of CSI, that’s probability of “T” assuming the relevant chance hypothesis generated it.

    P(T|H) is part of SPECIFICATION and it represents all relevant chance hypotheses.

    (2) If you sequenced the DNA of two women and find they they share the same allele in ~50% of sites that vary widely in the human population. Would you conclude it’s more probable that they are sisters than two people plucked at random from a population? Companies like 23andMe do precisely these calculations, btw.

    The tests that say two human sisters are related would show that neither are related to chimps.

  48. 48
    jcfrk101 says:

    Zachriel how is a Markov chain going to confirm anything but a tree like structure? The method is chosen because a tree like structure is assumed, so it will obviously confirm it.

  49. 49
    NickMatzke_UD says:

    26 Barry ArringtonNovember 23, 2015 at 4:55 pm

    wd400,

    Read the Berlinski quote.

    Nick is saying we can detect “sister” relationships even though we cannot detect “parent” relationships, which, of course, is incoherent.

    How about reading my actual blogpost, instead of the Berlinski quote? I actually explain how cladistics *does* test common ancestry, and supports common ancestry when the tests are positive (which is virtually always, with biological datasets). Read the parts about CI, null distributions, etc.

    I *also* say that cladistics successfully tests common ancestry, *despite* the fact that cladistic methods cannot detect direct ancestors, only collateral ancestors (sister-group relationships). The reason cladistics cannot detect direct ancestors is primarily because the computer methods propose trees where every taxon is a tip. Thus every tip can only be sister to other tips, you can never have a tip directly below another tip.

    As it happens, this limitation of cladistics has recently been overcome in modern Bayesian statistical phylogenetics. (Note carefully: cladistics is just one, fairly simple, form of phylogenetics. In fact, cladistics is considered old-fashioned at this point, even though it is useful for public debates with creationists since it is easier to explain than statistical likelihood calculations and Bayesian MCMC searches.) I predicted that direct-ancestor detection was coming in that blogpost in 2013, and lo and behold, it’s been published in 2014 and 2015. These new methods propose and test trees where some of the “tips” are moved into direct ancestor positions. You have to have a model of fossil sampling through time and some other computational machinery to make this work, which is why it’s taken so long.

    These new methods are cool, but they don’t change anything fundamentally. The terms “common ancestry” and “direct ancestry” mean different things. You can infer the first without having the second. Just like a DNA test can tell you if someone is your cousin, even if neither of you know who your grandparents were. Getting this confused is one of Barry’s mistakes, amongst numerous other failings (high arrogance, low knowledge, high propensity to blab without doing any research in the primary literature, reliance on quotes from popularizations rather than absorbing the consensus in the primary literature.)

    On testing common ancestry: the Berkeley page is only correct for a one-dataset, one-cladogram analysis. In such a situation, what you are doing is saying common ancestry is so well-supported generally in biology, that it is safe to assume it for for this particular analysis, rather than wasting time re-doing already-proven science. This is perfectly reasonable. But it’s not the full story. Introductory science sources often don’t have the full story, and plus, intro-science websites are often written by beginning grad students who haven’t learned everything yet.

    If for whatever reason, one wants to waste time arguing with ignorant creationists, cladistics *can* be used to test common ancestry. The simplest test is…run *two* different datasets! For example, two different genes, or a gene and a collection of many morphological characters, or whatever. Common ancestry predicts that the trees will be much more similar than expected by chance, because the characters being studied will have shared history for the part of a tree in which they were inside the same ancestral lineages (Note: *not* freaking identical.There are many different, known, observable, and unavoidable and thus expected stochastic processes in mutation, population genetics, etc., that can produce some disagreements).

    Of course, it’s even a simplification to say that two datasets is, by itself, a test of common ancestry. A comparison of two datasets is really just one datapoint. The *real* test is comparing dozens, hundreds or thousands of datasets. The conclusion is: the statistical signal of vertical inheritance is amazingly, fantastically good for eukaryotes, especially multicellular eukaryotes with protected germlines. (Even the claimed exceptions in prokaryotes etc. are mostly overblown — as are hybridization events in eukaryotes, which are typically between what are close relatives anyway.)

    A more complex test (non-cladistic) involves constructing a null distribution from the data and then seeing how many sigma above the null your actual observed data. Often data are 10+ sigmas above the null distribution of no tree pattern.

    Yet more complex methods involve fitting probabilistic models and using standard statistics like Likelihood Ratio Tests and Bayes Factors to compare the hypotheses of no common ancestry and common ancestry.

    The authors of this work are people like David Penny, and Doug Theobald (Nature, 2010). The work is *extremely* well-known to anyone serious who has followed the creationism issue. Much of the earlier work is laid out, with explanations and citations, in Theobald’s “29+ Evidences for Common Ancestry” FAQ at talk.origins, which has been online for 10+ years now.

    Anyone serious would know about all of this, and review and rebut it in detail, if they wanted to say anything serious about how common ancestry is not supported. But, Berlinski doesn’t do this, and neither does Barry Arrington. Why? Are ignorant, lazy, and arrogant words that are too strong for that kind of behavior?

  50. 50
    Gordon Davisson says:

    Virgil Cain @47:

    P(T|H) is part of SPECIFICATION and it represents all relevant chance hypotheses.

    You’ve got it backwards; the specification is part of P(T|H). Specifically, T is the specification, or target. H is a specific chance hypothesis. In general, you need to calculate P(T|H) under each of the relevant chance hypotheses, and you’ll get a different result for each one.

    Actually, it’s even more complicated than that, because any given event will satisfy many possible specifications, and you’ll generally get a different result under each combination of T and H.

    For instance, consider a poker hand consisting of the 10 through ace of spades. There are many specifications it satisfies (“natural royal flush in spades”, “royal flush”, “spades flush”, “flush”, “straight”, “natural straight”, “5 cards”, etc) and many possible chance hypotheses (dealt from a well-shuffled 52-card deck, a deck with one ace, a deck with two aces, a pinochle deck, high hand from 7 cards from various decks, various poorly-shuffled decks, etc). You’ll get a different P(T|H) for every different combination of specification and hypothesis!

    (BTW, you’ll generally get the highest CSI for that hand under the specification “flush”. “Royal flush” would obviously give a smaller P(T|H), but “flush” is shorter, and the decrease in specificational resources more than makes up the the increase in probability.)

  51. 51
  52. 52
    Barry Arrington says:

    Nick,

    Do you still believe that 500 coins on a table all heads would not really warrant a design inference?

    By the way, this comment still ranks as the number one most stupid thing that has ever been said on UD. I would call you a buffoon, but that would be an insult to buffoons everywhere.

  53. 53
    Barry Arrington says:

    Nick, do you still expect us to believe that you read Darwin’s Doubt and wrote a 9,300 word review of the book within ONE DAY of when the book became available for purchase.

  54. 54
    Barry Arrington says:

    Nick, with your record here (not even including all of the literature bluffs you’ve pushed here over the years), you still seem to expect us to believe you as a credible source on anything. How odd.

  55. 55
    StephenB says:

    Zachriel,

    Hypothesis-testing is not circular reasoning, even though it assumes what it is trying to show.

    No. A hypothesis is not an assumption.

    A hypothesis is a proposed explanation made on the basis of limited evidence as a starting point for further investigation. The explanation is established aposteriori (after the evidence is introduced).

    An assumption is a thing that is accepted as true without proof. The explanation is established apriori (before the evidence is introduced).

    If you don’t understand why “before” is different than “after,” let me know and I will try to explain it another way.

  56. 56
    Jack Jones says:

    “Much of the earlier work is laid out, with explanations and citations, in Theobald’s “29+ Evidences for Common Ancestry” FAQ at talk.origins, which has been online for 10+ years now.”

    That was dealt with long ago

    http://www.trueorigin.org/theobald1b.php#pred1

  57. 57
    Barry Arrington says:

    I shall summarize the Darwinists’ comments:

    “Tree” in this discussion is shorthand for the tree of life, i.e, common descent.

    1. Cladistics is a technique that they admit necessarily always results in at least some sort of tree.

    2. They employ cladistics and sure enough it produces a tree.

    3. Then they claim that the fact that it produced a tree establishes that trees necessarily must be produced.

    I say “but wait; how can a process that cannot possibly produce the result ‘non-tree’ be used to establish that ‘tree’ must necessarily be true?”

    Response: Ignorant, lazy, and arrogant, high arrogance, low knowledge, high propensity to blab without doing any research in the primary literature, reliance on quotes from popularizations rather than absorbing the consensus in the primary literature.

    Oh, well that explains it. Thanks.

  58. 58
    Gordon Davisson says:

    Barry @40:

    BTW Gordon,

    All ID proponents understand what an abductive inference is. Because design inferences are abductive in nature.

    There’s a big difference between using and understanding. Since you’re claiming that a standard abductive inference is circular, it’s clear that you at least do not understand abductive inference.

    If all you are saying is: “We have assumed common descent and we can often arrange the data in a way that is consistent with that assumption,” then who could disagree with that. When I said “establishes” in my original post it was clear I was talking about just that: establishes as a matter of fact.

    If you agree that cladistics does not establish common descent as a matter of fact, then we are in agreement (albeit apparently violent agreement). Now go tell Liddle.

    The success of cladistics in classifying organisms provides incredibly strong evidence for common ancestry. Whether you consider the tests of how well cladistic models match actual distributions of characteristics to be part of cladistics itself (in which case cladistics does support common ancestry, or whether you consider those tests to be outside of cladistics itself (in which case the support is not from cladistics itself, but whatever field you classified those tests into) is a semantic distinction not worth worrying about.

    Let me make it simple for you:

    Circular and invalid: “I can classify organisms based on the assumption of common ancestry; this supports common ancestry!”

    Non-circular and valid: “I can classify organisms based on the assumption of common ancestry and the results match the real distribution of organisms’ characteristics very very well; this supports common ancestry!”

    The key is drawing an inference from the hypotheses and testing it. Many many tests have been done, and the result is that common ancestry is very well supported.

  59. 59
    Barry Arrington says:

    Gordon,

    Since you’re claiming that a standard abductive inference is circular, it’s clear that you at least do not understand abductive inference.

    Go back and read my response again. This time for comprehension. I made no such claim.

  60. 60
    Barry Arrington says:

    Gordon,

    The success of cladistics in classifying organisms provides incredibly strong evidence for common ancestry . . .

    If one assumes common ancestry in classifying organisms in the first place.

    It really is stunning that Darwinists seem literally incapable of seeing the difference between the data and their assumptions about that data.

  61. 61
    wd400 says:

    Oh, this is where you’re going wrong.

    1. Cladistics is a technique that they admit necessarily always results in at least some sort of tree.

    2. They employ cladistics and sure enough it produces a tree.

    3. Then they claim that the fact that it produced a tree establishes that trees necessarily must be produced.

    1. Phylogenetic methods (cladistics is a narrower word, which has been used imprecisely in this thread) result in a tree (or a distribution of trees) and some measure of how will the data used to estimate that tree fits the particular tree

    2. close enough, remembering the extra stuff in (1).

    3. No one has claimed this. The support for common descent either comes from the consistancy with which the same tree is estimated from different data, how well the data fits the tree like structure and (in the case of explicit tests) how much better the bifurcating tree fits the data than some alternative hypothesis (the Theobald paper being an example).

  62. 62
    Barry Arrington says:

    Also, does anyone else believe that it is passing strange that I am the one quoting the DARWINIST literature and Nick and wd400 are the ones trying to explain away the literature from their own side?

    Nick: A primary purpose of cladistics is to establish common descent. The information from my own college’s website does not say that because . . . some ignorant graduate student wrote it. Yeah, that’s the ticket.

  63. 63
    Jack Jones says:

    “common ancestry is very well supported.”

    The philosophy of evolution can support any finding so it makes no sense to claim common ancestry is well supported, They accommodated the fossil sequence as it is and anyway they can appeal to convergence, even “cascades of convergence” or hgt, ghost lineages, evolution in leaps, loss of characters and replacement at high rate etc.

    And if that all fails then they will claim a bush of life and it won’t phase them either.

    Craig Venter said there is no tree but a bush and the late Will Provine rejected that there is a tree, he said it was a failure of the modern synthesis and yet he remained an Evolutionist.

    We are dealing with a philosophy here.

  64. 64
    Barry Arrington says:

    GD:

    But there’s a very similar non-circular version: make assumptions about evolution, derive resulting categorization from those assumption, find the result matches actual data;

    Gah! Of course the data will match the assumption. The data were arranged based on the assumption.

  65. 65
    Robert Byers says:

    YUP
    Evolutionists really do see common descent because they don’t imagine other options for likeness. Common design can predict these trees just as well. Then mechanisms also for details of population changes.

    Its been a careless flaw of investigation for evolutionists to insist eyeballs amongst everyone is proof of common descent for some creature with the original eyeballs. When God would also have created everything with eyeballs because its a good idea and it makes biology move within laws just like laws of physics.
    In like mammer all ideas of trees based on connecting likeness in limbs is just a giant assumption of CD. the likeness is not evidence of CD. Just a option of how to look at things. NOT scientific evidence.
    If evolutiuonism doesn’t embrace that common design would produce these trees also and so the trees should not be presented as settled fact for common descent then evolutionism loses intellectual investigative credibility.
    They must correct themselves and right quick.

  66. 66
    Box says:

    “The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous”

    [Zvelebil and Baum, “Understanding Bioinformatics”, 239]

  67. 67
    bornagain says:

    It is interesting to note just how far illusion and imagination play into Darwinian thinking.

    As highlighted in post 46, I hold cladistics to be a prime example that

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe

    Yet, despite the fact that Darwinists have no real time empirical evidence to appeal to to demonstrate the origination of even a single protein molecule by unguided material processes,,,

    Yockey and a Calculator Versus Evolutionists – Cornelius Hunter PhD – September 25, 2015
    Excerpt: In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein.,,,
    Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”
    Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.
    A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.
    These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.
    Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had.,,,
    http://darwins-god.blogspot.co.....ersus.html

    Despite that glaring poverty in real time empirical evidence, Darwinists still insist that the stunning integrated complexity in life is not really design but is merely ‘the illusion of design’

    “Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.”
    Richard Dawkins – “The Blind Watchmaker” – 1986 – page 21

    Life Reeks Of Design – Behe
    https://www.youtube.com/watch?v=Hdh-YcNYThY

    Now where this Darwinian claim that we are merely seeing the ‘illusion of design’ gets really interesting is in the fact that Darwinists also claim that our conscious mind, the most sure thing that we can know about reality, is also an illusion.

    “We have so much confidence in our materialist assumptions (which are assumptions, not facts) that something like free will is denied in principle. Maybe it doesn’t exist, but I don’t really know that. Either way, it doesn’t matter because if free will and consciousness are just an illusion, they are the most seamless illusions ever created. Film maker James Cameron wishes he had special effects that good.”
    Matthew D. Lieberman – neuroscientist – materialist – UCLA professor

    Atheists Don’t Really Exist:
    https://docs.google.com/document/d/14DktPLhEDt1rxJgUWbkpLCWuDZEJDz4xnrLLVfsXkk8/edit

    Thus, we have a perfect storm of imagination and illusion supporting grand Darwinian claims.

    First off, all grand Darwinian claims rest on undisciplined imagination.

    Secondly, despite having no real time empirical evidence for their imaginary claims, Darwinists insist that the overwhelming appearance of design we are seeing in life is not real but is merely an illusion.

    Thirdly, according to Darwinists, the ‘mind’ that is seeing this illusion of design, the thing we can be most sure about, is also an illusion itself.

    In other words, Darwinian evolution is so dependent on the imagination of man in order to try to make its case, instead of real time evidence to make its case, that in the end the mind of the Darwinist itself becomes pure imagination.

    Of related note: Darwinists themselves have undermined any truth claims they have for reality.

    The following interview is sadly comical as a evolutionary psychologist realizes that neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth, not even for the truth that he is purporting to give in the interview, (which begs the question of how was he able to come to that particular truthful realization, in the first place, if neo-Darwinian evolution were actually true?);

    Evolutionary guru: Don’t believe everything you think – October 2011
    Interviewer: You could be deceiving yourself about that.(?)
    Evolutionary Psychologist: Absolutely.
    http://www.newscientist.com/ar.....think.html

    Evolutionists Are Now Saying Their Thinking is Flawed (But Evolution is Still a Fact) – Cornelius Hunter – May 2012
    Excerpt: But the point here is that these “researchers” are making an assertion (human reasoning evolved and is flawed) which undermines their very argument. If human reasoning evolved and is flawed, then how can we know that evolution is a fact, much less any particular details of said evolutionary process that they think they understand via their “research”?
    http://darwins-god.blogspot.co.....their.html

    Why No One (Can) Believe Atheism/Naturalism to be True (Plantinga’s Evolutionary Argument Against Naturalism) – video
    Excerpt: “Since we are creatures of natural selection, we cannot totally trust our senses. Evolution only passes on traits that help a species survive, and not concerned with preserving traits that tell a species what is actually true about life.”
    Richard Dawkins – quoted from “The God Delusion”
    http://www.youtube.com/watch?v=N4QFsKevTXs

    Quote: “In evolutionary games we put truth (true perception) on the stage and it dies. And in genetic algorithms it (true perception) never gets on the stage”
    Donald Hoffman PhD. – Consciousness and The Interface Theory of Perception – 7:19 to 9:20 minute mark – video
    https://www.youtube.com/watch?feature=player_detailpage&v=dqDP34a-epI#t=439

    Of related note as to differentiating what is truly real from what is merely imaginary.

    In the following study, researchers who had a bias against Near Death Experiences being real, set out, in Darwinian tradition 🙂 , to prove that the experiences were merely hallucinations.
    They did this by setting up a clever questionnaire that could differentiate which memories a person had were real and which memories a person had were merely imaginary.
    They did not expect the results they got:

    ‘Afterlife’ feels ‘even more real than real,’ researcher says – Wed April 10, 2013
    Excerpt: “If you use this questionnaire … if the memory is real, it’s richer, and if the memory is recent, it’s richer,” he said.
    The coma scientists weren’t expecting what the tests revealed.
    “To our surprise, NDEs were much richer than any imagined event or any real event of these coma survivors,” Laureys reported.
    The memories of these experiences beat all other memories, hands down, for their vivid sense of reality. “The difference was so vast,” he said with a sense of astonishment.
    Even if the patient had the experience a long time ago, its memory was as rich “as though it was yesterday,” Laureys said.
    http://www.cnn.com/2013/04/09/.....periences/

    “More real than real?”,, That is quite an interesting comment for someone to make who believes his own mind is merely an illusion! 🙂

  68. 68
    Barry Arrington says:

    wd400,

    Are you going to address the 500 pound gorilla? UC Berkeley’s website Journey into Phylogenetic Systematics lists three uses of the techniques. None of those uses is “demonstrate common descent.

    Nick tries this cop out: Some ignorant grad student wrote it.

    Does that satisfy you?

  69. 69
    NickMatzke_UD says:

    Wow Barry, that’s like 5 replies from you, and none of them even respond to the points I made. In your replies:

    1. You made a mistake in your opening post, by confusing the terms “direct ancestry” and “common ancestry” in your discussion of my quote.

    2. No discussion of how comparing the trees from 2 or more different datasets constitutes a test of common ancestry, rather an assumption of it.

    3. No discussion of how null distributions can be constructed from the data, and the parsimony scores from those compared to the observed parsimony score on the original data (or CI, or other support statistics).

    4. No discussion of the probabilistic methods that have advanced beyond cladistics in terms of allowing the inference of direct ancestors, and in allowing formal probabilistic tests of common ancestry with the standard tools of statistical model choice (used in dozens or hundreds of different fields), including things like the Likelihood Ratio Test.

    5. No discussion of the previously published, well-known peer-reviewed literature on any of these topics.

    You exhibited no knowledge of any of these in your previous posts. Yet you blab about the topic anyway. And you refuse to admit your mistakes when they are pointed out, instead attempting to distract by bringing up other issues. If you want to know why scientists don’t take ID seriously: your behavior is an example of why.

  70. 70
    NickMatzke_UD says:

    The “non-cladistic” was supposed to go here in my post:

    Yet more complex methods involve fitting probabilistic models
    –>
    Yet more complex (non-cladistic) methods involve fitting probabilistic models

  71. 71
    Barry Arrington says:

    I have to pack for my Thanksgiving trip. I’m out until next Monday.

  72. 72
    wd400 says:

    Oh really Barry.

    This thread is now a cemetery for points that you advanced then suddenly forgot about when you were shown to be wrong. Instead of addressing any of these points you’ve employed the squid ink defence: a cloud of unrelated attacks on Nick to aid a quick retreat. But, while you ignore any point you like, it’s crucially important that others explain why a natural history museum chose to write what they did on their eduational materials?

  73. 73
    Gordon Davisson says:

    Barry @64:

    GD:

    But there’s a very similar non-circular version: make assumptions about evolution, derive resulting categorization from those assumption, find the result matches actual data;

    Gah! Of course the data will match the assumption. The data were arranged based on the assumption.

    The arrangement is based on the assumption; the data is not, and therefore the fit between arrangement and data is not.

    Try arranging cars under the assumption that they evolved via branching common ancestry. Seriously, try it. Then see how well actual cars fit your arrangement. Hint: however you arrange them, you’ll find many of their characteristics don’t match the arrangement well at all.

  74. 74
    mike1962 says:

    “if free will and consciousness are just an illusion”

    I always have to ask: consciousness is an illusion of what?

    Well, if consciousness is an “illusion”, whatever that might mean, then so is everything consciousness experiences. Including Darwinistic ideology. And pronouncements that consciousness is an illusion.

    Self-referential fail.

  75. 75
    bornagain says:

    The data does not, no matter how much Darwinists try to force fit it into their narrative, fit the assumption of common descent.

    a few notes on the ‘top down’ fossil record:
    https://docs.google.com/document/d/1tATBrfBdSX-HokFB2I9kOxZAXluKeVdrziMW2dloKs4/edit

    Logged Out – Scientists Can’t Find Darwin’s “Tree of Life” Anywhere in Nature by Casey Luskin – Winter 2013
    Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors.
    Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,,
    Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance:
    • A 1998 paper in Genome Research observed that “different proteins generate different phylogenetic tree[s].”6
    • A 2009 paper in Trends in Ecology and Evolution acknowledged that “evolutionary trees from different genes often have conflicting branching patterns.”7
    • A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history to be.”8
    Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled “Why Darwin Was Wrong about the Tree of Life.”9 The author quoted researcher Eric Bapteste explaining that “the holy grail was to build a tree of life,” but “today that project lies in tatters, torn to pieces by an onslaught of negative evidence.” According to the article, “many biologists now argue that the tree concept is obsolete and needs to be discarded.”,,,
    Syvanen succinctly summarized the problem: “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” ,,,
    “battles between molecules and morphology are being fought across the entire tree of life,” leaving readers with a stark assessment: “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”10,,,
    A 2012 paper noted that “phylogenetic conflict is common, and [is] frequently the norm rather than the exception,” since “incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.”12,,,
    http://www.salvomag.com/new/ar.....ed-out.php

    podcast – Molecular Data Wreak Havoc on (Darwin’s) Tree of Life – Casey Luskin – March 2014
    http://intelligentdesign.podom.....7_31-07_00

    Phylogeny: Rewriting evolution – Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. – Elie Dolgin – 27 June 2012
    Excerpt: “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree,” he says. “…they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist – Kevin Peterson)
    Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says.
    Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.
    http://www.nature.com/news/phy.....on-1.10885

    etc.. etc.. etc..

  76. 76
    Gordon Davisson says:

    The data does not, no matter how much Darwinists try to force fit it into their narrative, fit the assumption of common descent.

    We just had this conversation, over on the “Can a Lowly Lawyer Make a Useful Contribution? Maybe” thread. Remember? You spewed a bunch or random links and quotes you thought supported your case, I picked one (“Contradictory Trees: Evolution Goes 0 For 1,070”, about building trees based on 1,070 different genes and getting 1,070 different trees), pointed out that the analysis was done in a way that’d give much noisier data (over 30x!) than the usual method, and the discrepancies between trees matched what I’d expect from noisy data, and also that despite the noise the 1,070 trees still matched each other much better than 1,000 trees built from random data did.

    Now you’re spewing more links. Have you checked into them any further than the last batch? Based on the last one (microRNAs), it doesn’t look like it. According to a later article in Nature News (“Flaws emerge in RNA method to build tree of life”), the microRNA didn’t work as well as Peterson hoped, and corrected analyses match the standard trees much better.

    …Which actually refutes Barry’s original claim. If this was all as circular as he thinks, we wouldn’t be able to find discrepancies between different trees; all that would be magiced away by the assumption of evolution and common ancestry. But it’s not; we can test different methods against each other, we can check their internal assumptions (one of the things that turned up problems with the original microRNA method), etc. These tests are possible, and are done; and while the trees aren’t perfect (real data never is), they’re far better than can be explained without common ancestry.

  77. 77
    bornagain says:

    I remember the discussion very well. It seems you ‘imagine’ a very different discussion than the one I do, for instance:

    A few more notes in regards to the SEVERELY incongruent sequence data:
    http://www.uncommondescent.com.....ent-588372

    Gordon Davisson, your idea of what constitutes real time empirical evidence and what real time empirical evidence actually is are two VERY different things.
    http://www.uncommondescent.com.....ent-588425

    http://www.uncommondescent.com.....ent-588411

    Discordant ORFan Data
    http://www.uncommondescent.com.....ent-588392

    Moreover, we have ample reason to believe that the genetic data is being ‘cherry picked’ by Darwinists to accord to the preconceived Darwinian narrative (and is therefore to be held to be untrustworthy and suspicious in its overall integrity):
    http://www.uncommondescent.com.....ent-588287

    Moreover, your claim that the sequence data is not really severely discordant with Darwinian claims just took a severe blow:

    Unexpected features of the dark proteome – Oct. 2015
    Excerpt: Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions,,,
    We deliberately chose this stringent definition of “darkness,” so we can be confident that the dark proteome has completely unknown structure.,,,
    ,,,in eukaryotes and viruses, about half (44–54%) of the proteome was dark (Fig. 1B). Of the total dark proteome, nearly half (34–52%) comprised dark proteins.
    We repeated the above analysis using an even more stringent definition for darkness—combining PMP (2) and Aquaria (SI Methods) — but this had little effect (Fig. S1).,,,
    Lower Evolutionary Reuse.
    For each protein, we calculated how frequently any part of its sequence has been reused across all other known proteins (SI Methods). Dark proteins were reused much less frequently than nondark proteins (Fig. 4 C and Fig. S8), suggesting that dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches. This result was partly expected, given how darkness was defined and given the progress of structural genomics in targeting large protein families with unknown structure (8). Low evolutionary reuse also partly explains why dark proteins have few known interactions (Fig. 4 B and Fig. S8), because many interactions are inferred by homology (33).
    http://www.pnas.org/content/ea.....2.full.pdf

    The Dark Proteome and Dark Evolution – Evolution Did It – Cornelius Hunter – Nov. 23, 2015
    Excerpt: “Thus, our results suggest that many of the uncharacterized orphan sequences … are indeed real proteins.”
    http://darwins-god.blogspot.co.....ution.html

    And to remind readers, Darwinists cannot even explain how a single protein was created by unguided material processes, much less half the proteome:

    http://www.uncommondescent.com.....ent-589507

  78. 78
    Bob O'H says:

    Barry @ 57 –

    I say “but wait; how can a process that cannot possibly produce the result ‘non-tree’ be used to establish that ‘tree’ must necessarily be true?”

    As Nick explained in 49: if you produce trees for the same species, independently using different data, you won’t get the same (or very similar) trees if the assumption of common descent is wrong.

  79. 79
    EugeneS says:

    Bob O’H @78

    If I understand correctly, you are saying that common ancestry can be independently verified by measurements.

    Assumptions are always assumed, never verified. A theory never tests its own assumptions. It’s basic logic.

    In this particular case, all that can happen, is something warrants a revisit of a particular previously constructed (sub)-tree. But in any case it will be a tree, i.e. the assumption of common ancestry is not put to test.

  80. 80
    Bob O'H says:

    EugeneS @ 79 –

    Assumptions are always assumed, never verified. A theory never tests its own assumptions. It’s basic logic.

    I’m afraid your logic is faulty. We can test assumptions made by a theory by comparing it to data, e.g. by comparing the fit.

    As a practical example, we can assume a linear relationship between x and y and fit a straight line (e.g. by least squares). We can then verify the assumption by looking at the differences between the data and the fitted line: if the linearity assumption is true, we won’t see any pattern. Anscombe’s quartet is a nice visual demonstration of this.

  81. 81
    Box says:

    Nick Matzke #49: If for whatever reason, one wants to waste time arguing with ignorant creationists, cladistics *can* be used to test common ancestry. The simplest test is…run *two* different datasets! For example, two different genes, or a gene and a collection of many morphological characters, or whatever. (…) The *real* test is comparing dozens, hundreds or thousands of datasets. The conclusion is: the statistical signal of vertical inheritance is amazingly, fantastically good for eukaryotes, especially multicellular eukaryotes with protected germlines. (Even the claimed exceptions in prokaryotes etc. are mostly overblown — as are hybridization events in eukaryotes, which are typically between what are close relatives anyway.)

    “Amazingly fantastically good”, according to Nick Matzke. Okay, now read Bornagain’s posts #75 #77. I have extracted a few quotes:

    “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree, (…) they give a totally different tree from what everyone else wants.” (Elie Dolgin)
    “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” (Syvanen)
    “incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.” (Davalos)
    “the holy grail was to build a tree of life,[but] today that project lies in tatters, torn to pieces by an onslaught of negative evidence. (…) many biologists now argue that the tree concept is obsolete and needs to be discarded.” (Bapteste)
    “evolutionary trees from different genes often have conflicting branching patterns.” (Degnan)
    “What we know at this stage is that we do have a very serious incongruence, (…). It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.” (Pisani)

  82. 82
    EugeneS says:

    Bob,

    The way you interpret the data always depends on key basic assumptions.

    Assumptions can be verified but it is always done outside of a theory. Within a given theory it is not possible.

    By doing least squares etc. you can assert something but again based on certain assumptions.

    I think there are no measurements you can put to test common ancestry with. All that can ever happen is: ok, we made a mistake, species A is closer to species B than to C. That’s all. There is no way even theoretically to measure something and see if species A and species B do not belong to the same tree. You just assume they do before you measure anything. All your measurements can ever change is relative proximity of A and B in a single tree.

    You assume common ancestry and based on this assumption you will then “correct” the picture using new more accurate data.

    I cannot see anything which can be used to independently assess the validity of the assumption of common ancestry. E.g. how will you ever know if there was one tree or a forest starting off very similar genomes but unrelated via ancestry?

  83. 83
    Cabal says:

    To the question (not addressed at me)

    Do you still believe that 500 coins on a table all heads would not really warrant a design inference?”

    my layman’s opinion would be:

    Since all posible combinations of 500 coin heads on the table have the same probability of occurence, I’d only note the 500 heads as a very rare event -, and yet it is not inonceivable that the next throw would show the same result – but the chances of that happening are not too bright.

    I just presume that statisticians and game theorists are among the best qualified to judge and arbitrate in such matters. But I am that rare specimen who prefer listening to people with a career encompassing the subject.

    I am a nobody, and I would rate plumbers, dentists or real estate brokers or even Donald Trump to share essentially the same level of competence on this matter. Even as a nobody, I have at least done my best to love and study science for most of my 85 years, say since 1943.

    Thinking of noone in particular, I tend to see a tendency among science critics to underestimate the quality of most scientists, often resulting in downright denial of what may be a rather well established fact accepted by most people – as for instance WRT the age of the Earth, they chose to adopt the YEC POW. All people should be free to believe whatever they want. I only state may position.

    WRT the controversy between ID and mainstream science, to me the words of Kipling wrt the East vs. the West comes to mind.

  84. 84
    Jack Jones says:

    In 2008, William B. Provine, Cornell University historian of science and professor of evolutionary biology, stated that “every assertion of the evolutionary synthesis below is false“

    “10. Evolution is a process of sharing common ancestors back to the origin of life, or in other words, evolution produces a tree of life.”
    William Provine, Random Drift and the Evolutionary Synthesis, History of Science Society HSS Abstracts.

    Craig Venter ” Well I think the tree of life is an artifact of some early scientific studies that aren’t really holding up. So the tree, you know, there may be a bush of life. … So there is not a tree of life.”

    http://thesciencenetwork.org/p.....life-panel

  85. 85
    Bob O'H says:

    EugeneS –

    By doing least squares etc. you can assert something but again based on certain assumptions.

    Yes, but that assertion has consequences. It makes specific predictions about the data (e.g. a straight line fit),which we can test. This might be that the deviation between the (fitted) model and data is noise (Anscombe’s quartet is a nice example of how this can be tested). Or it might be that when the model is fitted to replicate data, the estimated parameters (e.g. a tree) will be congruent.

    I think there are no measurements you can put to test common ancestry with. All that can ever happen is: ok, we made a mistake, species A is closer to species B than to C. That’s all.

    Under an assumption of common ancestry, if we do that for several genes, we will consistently see that A is closer to B than C. But if there is no common ancestry, we will often see that A is closer to C. Thus congruence of the estimated tree for several data sets (i.e. genes) is a test of the underlying theory.

  86. 86
    bornagain says:

    Darwin’s (failed) Predictions – Cornelius G. Hunter – 2015

    *(failed)Common descent predictions
    The pentadactyl pattern and common descent
    Serological tests reveal evolutionary relationships
    Biology is not lineage specific
    Similar species share similar genes
    MicroRNA

    *(failed)Evolutionary phylogenies predictions
    Genomic features are not sporadically distributed
    Gene and host phylogenies are congruent
    Gene phylogenies are congruent
    The species should form an evolutionary tree

    *(failed)Evolutionary pathways predictions
    Complex structures evolved from simpler structures
    Structures do not evolve before there is a need for them
    Functionally unconstrained DNA is not conserved
    Nature does not make leaps
    https://sites.google.com/site/darwinspredictions/home

  87. 87
    Virgil Cain says:

    Gordon Davisson:

    You’ve got it backwards; the specification is part of P(T|H).

    The equation is for SPECIFICATION, not CSI. Taty was my point.

    In general, you need to calculate P(T|H) under each of the relevant chance hypotheses, and you’ll get a different result for each one.

    That’s if someone can propose a hypothesis. That is the whole problem- not one of ID’s opponents can support their position.

  88. 88
    Virgil Cain says:

    Matzke:

    I *also* say that cladistics successfully tests common ancestry,

    Unfortunately it doesn’t test common ancestry. It can’t as no one knows how to produce the changes required.

  89. 89
    Virgil Cain says:

    The concept of common ancestry is untestable. No one knows what makes an organism what it is and there isn’t any evidence that changes to DNA can produce all of the physiological and morphological changes required.

    The DNA tests that show human family members are related would not show those family members are related to chimps.

  90. 90
    Zachriel says:

    jcfrk101: how is a Markov chain going to confirm anything but a tree like structure? The method is chosen because a tree like structure is assumed, so it will obviously confirm it.

    Because we can provide a statistical test of how well the data fits the posited tree. We can also compare different sets of data to see if they show the same tree.

    Barry Arrington: Do you still believe that 500 coins on a table all heads would not really warrant a design inference?

    Coins are artifacts. Would you believe trillions of atoms all geometrically aligned?

    StephenB: No. A hypothesis is not an assumption.

    Semantics.

    hypothesis, a tentative assumption made in order to draw out and test its empirical consequences

    StephenB: A hypothesis is a proposed explanation made on the basis of limited evidence as a starting point for further investigation. The explanation is established aposteriori (after the evidence is introduced).

    In hypothetico-deduction, the basis of the scientific method, the hypothesis is the tentative assumption, and entailments are deduced from the hypothesis. It takes the form if H then E.

    StephenB: An assumption is a thing that is accepted as true without proof. The explanation is established apriori (before the evidence is introduced).

    The hypothesis is tentatively accepted as true in order to deduce its entailments, which are then subject to verification.

    For instance, if we hypothesize the Earth rotates, from the assumption of the Earth’s rotation, we can make a series of deductions, that we should observe the retardation of the pendulum near the equator. We then test that entailment to either support or falsify the hypothesis.

    Barry Arrington: 3. Then they claim that the fact that it produced a tree establishes that trees necessarily must be produced.

    It produces a *strongly supported* tree for many different data-sets.

  91. 91
    Virgil Cain says:

    Zachriel is such a bloviating TARD. It has to be the most dishonest and deceptive evo alive.

  92. 92
    wd400 says:

    Hey Cabal,

    Since all posible combinations of 500 coin heads on the table have the same probability of occurence,…

    If all posible combinations of 500 coins are equiprobable then the rest of your post is fine. The problem with Barry’s post (as pointed out in that thread) is that he never specifies the processes by which the coins where placed. As it stands the question is akin to a famous “paradox” in probability theory and evidence that probability calculations can only be applied to well-posed questions.

    That Barry can still be so wrong and so angry about that post really is something.

  93. 93
    Virgil Cain says:

    wd400- If your position had something positive to say you wouldn’t have to flail away at ID. That you are forced to flail away at ID is a great indicator that your position has nothing.

  94. 94
    wd400 says:

    What are you on about Joe? Doesn’t seem to be related to anything I’ve said…

  95. 95
    Virgil Cain says:

    Typical cowardly non-response.

  96. 96
    kairosfocus says:

    WD400:

    I offer you a bet.

    There is a sealed video tape on how 500 coins ended up all H.

    What odds would you be prepared to bet at, that they came that way by a fair coin toss?

    What does your answer tell us about relative statistical weight of clusters of microstates, and the predominant cluster near 50-50 H and T in no particular order or organisation?

    And, what does it tell us about what FSCO/I is pointing to to moral certainty?

    KF

    PS: In case you wonder, L K Nash used the coins example to introduce statistical thermodynamics, and its undergirding of the law of thermodynamics. And yes, there are reasonable clusterings of microstates.

    PPS: In case you doubt the relevance of this to physical settings, my Mandl uses a model paramagnetic substance with parallel and antiparallel alignments, to do effectively the same.

  97. 97
    Jack Jones says:

    @96 KF

    That they would even dispute the scenario that 500 coins were all Heads deliberately just shows what an emotional commitment they have to their faith, In another scenario, say somebody bet them that they could flip a coin and get 50 heads in a row. I doubt they would even get up to 10 flips of heads in a row without the design denier coming to the conclusion that a fair coin was not being used.

  98. 98

    Can I point out that there are two different uses of the word “assumption” being used here? One is near to something like “axiom”. It is not axiomatic that two variables have a linear relationship or that morphological characters are distributed as a tree.

    The other is something like “hypothesis” as in “let as assume, for the purposes of this discussion, that there is a linear relationship between these two variables/these organisms have a common ancestor; if our assumption were correct, what would we we see? if it were not, how likely would we be to see the same thing?”

    It is the latter sense in which people sometimes phrase a hypothesis such as a linear/tree hypothesis as an “assumption”. The assumption is not an AXIOM. More importantly, the assumption itself is the subject of the test, and the default – the hypothesis that the test actually seeks to falsify, is the hypothesis that there is NO underlying linear relationship/underlying tree relationship and that any apparent slope or tree is simply a result of chance.

    That is why you cannot conclude common descent from a poorly fitting or inconsistent tree. You test common descent by seeing how well a tree will fit. If it doesn’t, your hypothesis is not supported.

    This is why there is no circularity. This is why it is possible to test the hypothesis of common descent. This is why we can be so sure of common descent – because the tree fit is so good.

    It’s so good that we can even see where there are small violations of the tree, and investigate why this should be the case. Hybridisation is one violation; horizontal gene transfer vectors are another.

    And those very exceptions are themselves “proof” (in the original sense of “tests”) of the common-descent rule – we find hybridisation most commonly near nodes – the further apart groups are on branches, the less commonly we observe evidence of hybridisation. We also find horizontal gene transfer in very specific patterns that themselves provide evidence of their non-vertical origin.

    And this is why, of course, that Common Descent is so widely accepted, even among IDists. Even YEC’s accept common descent of very large groups, or “baramins” – they just propose many trees rather than one (the “orchard”).

  99. 99
    Virgil Cain says:

    Common Descent cannot be tested, Elizabeth, and evolution is too complex to produce nice neat trees. OTOH a common design would expect trees that are constructed based on shared characteristics.

    But yes, knowledgeable people have known that YECs accept that evolution occurs and that darwin argued against a strawman.

  100. 100
    wd400 says:

    Are you trying to prove my point KF?

    When the random process (“that they came that way by a fair coin toss”) is specified you can work with probabilities. When it’s not you can’t.

    What on earth “Moral certainty” has do with any of this I can’t imagine (but please don’t waste your time composing one of your posts about it).

    Joe,

    Cowardly response to what? I really don’t have the foggiest idea of what you are talking about.

  101. 101
    Virgil Cain says:

    wd400- If you could support evolutionism, ie the claim that natural selection, drift, and constructive neutral changes, can produce the diversity of life, then you wouldn’t need to address any other ID arguments. The fact that you are compelled to flail away at the other ID arguments is evidence that you have nothing else.

    cheers,
    Virgil Cain

  102. 102
    Jack Jones says:

    @100

    If you came across 500 coins on a table all heads up then you wouldn’t bet they came that way by chance.

    If somebody challenged you your house then you wouldn’t take the bet, I doubt you would take the bet at even $50.

  103. 103
    wd400 says:

    Jack, can you answer Bertrand’s question?

    https://en.wikipedia.org/wiki/Bertrand_paradox_(probability)

    It’s very relevant to your post, because you seem to think “by chance” has a single well-defined meaning. But that’s not the case. Even Dembski makes this point in defining the CSI and requiring P(T|H) as part of that calculation.

  104. 104
    kairosfocus says:

    WD400, that is called splitting hairs to make an argument or even perhaps an excuse. No reasonable man coming upon a table with 500 coins all H will but conclude the least likely explanation is they were so by chance and such an outcome is as likely as any other. In fact, there is a specification that is shortly describable, “500 coins all H,” and there is a clustering of possible outcomes which makes it maximally unlikely that any reasonable chance hypothesis relevant to coins on a table would create such an outcome within the ambit of atomic and temporal resources of the observed cosmos . . . coin flipping is going to be much slower than fast organic reactions. Nor do you actually need to define a precise probability calculation to see this, the needle in haystack search challenge on the config space would instantly and intuitively show that this is maximally unlikely on chance and would only be plausible — note the distinct terminology — on design. For instance, the design of double headed coins, or the design of setting the coins or of having a biasing mechanism sufficient to make what would otherwise be utterly improbable likely. The fact that you are unwilling to give odds to take such a bet therefore speaks volumes. You know it is not realistic to appeal to chance for such a functionally specific, and complex in the sense of deeply isolated in a config space, outcome. KF

    PS: Another way of putting it is that if a judge sentences you to stay in gaol till under scrutiny with a fair coin you toss 500 H, he is effectively giving you a life sentence.

    PPS: If you don’t know or wish to dismiss and mock what moral certainty means in this sort of context, that too speaks volumes. And no, I will not waste time “throwing pearls . . . ” (FYI, if I were to compose a significant discussion, it would be mainly for the onlooker who genuinely wishes to learn.)

    PPPS: In this context too, by chance has an intuitive meaning that is sufficient to bring out a credibly non-foresighted, reasonably or highly contingent outcome that is subject to factors not within a relevant scope of analysis or control and which is similar to a tossed die or the like. Where, coin flipping is a classic, classic case in point. Indeed, a coin is in effect a two sided die that under fair conditions is a classic example of 1:1 flat random odds on flipping. As was known all along.

  105. 105
    wd400 says:

    KF, you too are welcome to answer Bertrand.

  106. 106
    Jack Jones says:

    “https://en.wikipedia.org/wiki/Bertrand_paradox_(probability”

    I don’t get the terminology being used.

    “It’s very relevant to your post, because you seem to think “by chance” has a single well-defined meaning.”

    Look at 104 and KF’s post on this issue, he says it better than I could.

  107. 107
    Zachriel says:

    kairosfocus: No reasonable man coming upon a table with 500 coins all H will but conclude the least likely explanation is they were so by chance and such an outcome is as likely as any other.

    Of course, because they’re artifacts, we presume they were placed there by their artisans. Not much of a stretch. If you look at the coin, it may even have a picture of a representative of the species.

  108. 108
    wd400 says:

    I don’t get the terminology being used.

    If it’s a matter of dragging yourself back to highschool geometry don’t worry too much, the pictures sum it up pretty well.

    Look at 104 and KF’s post on this issue, he says it better than I could.

    This is a shame,because KF says nothing.

  109. 109
    kairosfocus says:

    Z, with all due respect, that’s another dodge. The relevant context is not whether coins are artifacts, but the contingency of H/T uppermost. The same would obtain for a paramagnetic substance of 500 atoms with the atoms capable of going parallel or antiparallel to a B field, and the odds of finding them all N up, i.e. parallel sense, would be just as implausible on chance. And, per my allusion to Mandl, that was also put on the table. KF

  110. 110
    kairosfocus says:

    WD400, your dismissal above speaks volumes, and reveals the deep hostility to the design inference that drives it. In effect, you are trying to make an absurd position seem reasonable. Telling. KF

    PS: The above becomes especially plainly a case of arguing endlessly, as in a well known intro text on statistical thermodynamics, L K Nash opens up by discussing, you guessed it, coins and the distribution of outcomes to give an understanding of thermodynamic equilibrium and fluctuations etc. And no, he does not go into utterly irrelevant mental gymnastics to duck and dodge the force of the matter.

  111. 111
    Eric Anderson says:

    wd400:

    I fear you may be missing the point. Bertrand’s paradox is not really relevant to the discussion:

    The example of a coin toss is often used in probability examples to highlight the simple analysis of the resulting string. In other words, the example is used precisely to eliminate all the potential things that could go wrong with a real-world experiment, so that we can focus on the outcome and not get bogged down with experimental nuances of the coin, the machinery used to flip it, and on and on. That is why in the coin toss example it is assumed that it is a “fair coin,” etc.

    We can’t just throw the example out the window by complaining that the precise underlying mechanism is unknown. The “mechanism” has been put forward as a flip of a fair coin. That is all the mechanism that is needed for this example.

    Think of it this way. A “fair” flip of a “fair” coin is the proposed mechanism on the table. And we know enough about how that proposed mechanism operates to be able to determine whether that mechanism is likely to generate the result we see. In the case of 500 heads it clearly is not likely to be the mechanism at work.

    In contrast, we know of another mechanism — intelligent choice — that can easily produce the effect in question.

    We have plenty of information about the mechanisms in this case. So the whole concern about Bertrand’s paradox is misplaced.

    —–

    That said, let me add one additional practical point:

    The example of 500 heads as indicia of design is not a great example. Why? Because there is another competing explanation that is easily able to account for 500 heads: namely law/necessity. In other words a not-fair coin.

    Some people who put forward the 500 heads example carefully define that away by making sure the reader understands we are dealing with a “fair” coin. But using 500 heads in the first place just adds confusion. Also, we can then debate whether the flipping mechanism had some law/necessity bias to it.

    Much better would be to posit a flip of coins that resulted in, say, the first 50 prime numbers or something. Then the example would avoid much of the definitional baggage that accompanies a 500 heads example.

    Regardless, we don’t need to get hung up on hyper-skeptical navel-gazing over the example. Just take the example for what it means and have a reasonable discussion . . .

  112. 112
    wd400 says:

    We have plenty of information about the mechanisms in this case

    The “mechanism” has been put forward as a flip of a fair coin.

    Think of it this way. A “fair” flip of a “fair” coin is the proposed mechanism on the table

    You should read the post before commenting on it. Literally the only thing specified about the mechanism generating the pattern is that there was “no flipping involved”.

  113. 113
    Zachriel says:

    kairosfocus: The relevant context is not whether coins are artifacts, but the contingency of H/T uppermost.

    http://www.webelements.com/sod.....cture.html

    There are many odd correlations in nature, so the evidence that the coins are artifacts is certainly part of the question. It’s because we know about coins and their makers that we reach the conclusion that someone put the coins all heads up.

    Eric Anderson: Some people who put forward the 500 heads example carefully define that away by making sure the reader understands we are dealing with a “fair” coin.

    Or a steel coin in a strong magnetic field, but as we are dealing with a human artifact (Lincoln on the penny), we wouldn’t expect a strong magnetic field to accidentally rearrange all the coins.

  114. 114
    Jack Jones says:

    “It’s because we know about coins and their makers that we reach the conclusion that someone put the coins all heads up.”

    You’re missing the point which for you is not anything new.

    We know scrabble letters are designed too but if we came across a sentence of scrabble letters in the grass spelling out the sentence, “To be or not to be, that is the question”

    Then we would know that those scrabble letters were not just spilled there by accident or flung out randomly.

    And we wouldn’t propose that the sentence was formed by the letters being blown about by the wind.

  115. 115
    Zachriel says:

    Jack Jones: We know scrabble letters are designed too but if we came across a sentence of scrabble letters in the grass spelling out the sentence, “To be or not to be, that is the question” Then we would know that those scrabble letters were not just spilled there by accident or flung out randomly.

    Sure. We have artifacts, artisans, language, etc. All the evidence indicates that a peculiar species of ape was involved.

  116. 116
    Virgil Cain says:

    All the evidence indicates that a peculiar species of ape was involved.

    Nope, just humans. But that misses the point entirely. Leave it to Zachriel to avoid the issue and post a distraction.

  117. 117
    Virgil Cain says:

    It’s because we know about coins and their makers that we reach the conclusion that someone put the coins all heads up.

    So if they weren’t all heads we could infer it was all an accident? Really?

  118. 118
    Eric Anderson says:

    wd400:

    Please clarify your complaint.

    It seemed you were trying to make a substantive point about the 500-coin-heads type of examples and how Bertrand’s Paradox relates. My bad.

    It now appears you are simply complaining that the way the 500-coin-heads example was raised was not clear enough for your liking.

    —–

    So, are you making a substantive point with your repeated links to Bertrand’s Paradox, or are you just nitpicking the way someone worded the example? If the latter, then perhaps just asking for a clarification would be the way to go?

  119. 119
    John S says:

    someone stops by my house and says I’m taking you for a ride. I assume it’s in a car. I’m blindfolded and dropped in a bucket seat, I connect a seat belt. I hear an engine, i feel a rolling sensation, I sense turning, i feel a breeze from the window. I feel braking and acceleration. I hear the Doppler effect out the window. I hear squealing brakes, hear a motor stop. Every observation affirms my assumption, therefore I have proven it’s a car.

    Then I remove blindfold to find I’ve been taxiing around in an airplane. What is so difficult about understanding that you can’t prove what you assume? Unless you are claiming to have all knowledge. If you are going to say I had no blindfold in the example and nothing is hidden but all laid bare before me. I apologize to you, great God of all, for your assumption was no assumption at all.

    This isn’t an issue of logic it is an issue of pride. The preeminent and underlying assumption is that there can be no God (intelligence). Though it cannot be disproved it cannot be entertained even for a moment. This is the assumption that biases and blinds.

  120. 120
    Jack Jones says:

    @116 Virgil “Nope, just humans. But that misses the point entirely. Leave it to Zachriel to avoid the issue and post a distraction.”

    I gave him a chance Mr Cain, But what can ya do with somebody like that?

  121. 121
    wd400 says:

    Well, EA, again you should read the threads before you comment on them. My comment in 92 could hardly be clearer.

  122. 122

    John S: “What is so difficult about understanding that you can’t prove what you assume?”

    Nothing. What seems to be difficult is understanding that if you test the hypothesis that data have a tree-distribution you are testing probability of your best tree-fit under the null hypothesis that there is no underlying tree. Therefore, what is done is the complete opposite of proving what you assume. What you ASSUME is that the null is true – and you fit your tree model under that assumption. If the best trees you can fit are highly likely under that null, then you retain the null Only if your best tree is highly UNLIKELY under your null (which is your technical starting assumption) can you reject that null, and conclude that there really is an underlying tree structure in the data. Which clearly there is – as was noted by Linnaeus.

    JohnS: “This isn’t an issue of logic it is an issue of pride. The preeminent and underlying assumption is that there can be no God (intelligence). Though it cannot be disproved it cannot be entertained even for a moment. This is the assumption that biases and blinds.”

    Not at all. It has nothing to do with God, belief in, or otherwise. The assumption of a null-hypothesis test is that the null is true. You test how likely your data are under that assumption. If they are very unlikely, you can reject your null. The problem with God as a hypothesis arises if the hypothesised God is postulated to be omnipotent. You can’t then make a predictive hypothesis, so you also can’t derive a null.

    It’s not bias against the idea of God, it’s just a feature of scientific methodology that it can’t test unfalsifiable hypotheses.

  123. 123
    Phinehas says:

    AC:

    That is why you cannot conclude common descent from a poorly fitting or inconsistent tree. You test common descent by seeing how well a tree will fit. If it doesn’t, your hypothesis is not supported.

    If it is a tree, then isn’t it demonstrating common descent by definition? Every tree will have a base node from which all the other nodes descend. Given this, how is it possible for a tree not to demonstrate common descent?

  124. 124
    kairosfocus says:

    If in the end this were not so sadly revealing, it would be amusing. As in word of the day

  125. 125

    Phinehas: “If it is a tree, then isn’t it demonstrating common descent by definition? Every tree will have a base node from which all the other nodes descend. Given this, how is it possible for a tree not to demonstrate common descent?”

    Two points:

    First: If your best fit tree is a poor fit, or if resampling the data gives inconsistent trees, then it doesn’t matter that there is a tree that will fit, just as it doesn’t matter in a correlation that there is a non-zero slope line that will fit. What you calculate is the probability of that tree under the null hypothesis of “no underlying tree”. And if you retain your null, that means you cannot conclude that there is an underlying tree, even if you manage to find a poorly fitting one (or several equally badly fitting ones).

    Second: Even if you DID find an underlying tree (as Linnaeus did, without benefit of modern computing) it remains an observation to be explained. Common descent with modification, as Darwin proposed is one such explanation (but required a further explanation for the “modification” part which was what the rest of his theory addressed). But it is not the only explanation. I can’t think of another off-hand, but just because a theory accounts for a pattern does not mean the theory is correct.

  126. 126
    Virgil Cain says:

    Elizabeth B Liddle- Linnaeus’ tree was based on a Common Design. It had nothing to do with Common Ancestry.

  127. 127

    It was based on observation.

  128. 128
    Virgil Cain says:

    Elizabeth:

    Common descent with modification, as Darwin proposed is one such explanation

    It is a proposed explanation. However it doesn’t have any evidentiary support. And a common design would expect an orderly tree whereas evolution via drift, neutral changes and natural selection would not.

  129. 129
    Virgil Cain says:

    Elizabeth:

    It was based on observation.

    It was what he said was expected of a Common Design.

  130. 130
    Virgil Cain says:

    One would expect a priori that such a complete change of the philosophical basis of classification would result in a radical change of classification, but this was by no means the case. There was hardly any change even in method before and after Darwin, except that the “archetype” was replaced by the common ancestor- Ernst Mayr

    From their classifications alone, it is practically impossible to tell whether zoologists of the middle decades of the nineteenth century were evolutionists or not. The common ancestor was at first, and in most cases, just as hypothetical as the archetype, and the methods of inference were much the same for both, so that classification continued to develop with no immediate evidence of the revolution in principles. …the hierarchy looked the same as before even if it meant something totally different.- Gaylord Simpson

    Linnaeus’ classification represented a Common Design- and still does.

  131. 131

    I am not aware of his thinking regarding an explanation for what he observed; my point is that he based his taxonomy on observed morphological characteristics. He did not base it on any theory as to what the pattern should be.

  132. 132
    Virgil Cain says:

    The US Army can be and is also laid out as a branching tree. Do evolutionists think that Darwin’s mechanisms plus drift* and neutral changes produced it too?

    *assuming Moran’s position that Darwin didn’t include drift

  133. 133
    Virgil Cain says:

    Elizabeth B Liddle- Linne was in search of the Created Kinds and his classification was supposed to be a reflection of the Creator’s Common Design.

  134. 134
    Virgil Cain says:

    The Dewey Decimal System also produces a branching tree pattern. Do evolutionists think that Darwin’s mechanisms plus drift* and neutral changes produced it too?

    *assuming Moran’s position that Darwin didn’t include drift

  135. 135

    And the Dewey Decimal System is a designed pattern, right, designed to make books easier to find.

    So that’s another candidate explanation for the observed pattern of morphological characters in living things – just as Dewey caused books to have patterns of decimal digits stamped on their spines, so an Intelligent Designer designed living things to be easy to find, by giving them easily catalogued characteristics.

    As I said to Phinehas: the observation of a tree-pattern (which is quite incredibly strong) does not mean that common descent is true. Common descent is an explanation for something that had already been observed. It wasn’t an a priori prediction because nobody thought of common descent until AFTER the tree was found.

    However, however, failure to find tree patterns would falsify common descent, at least probabilistically, which is as good as falsification actually gets in science. That’s why the fabled rabbit-in-the-Cambrian would be such a problem. It would seriously muck up the tree predicted by common descent. As indeed the HGT signal did – and showed that longitudinal descent is not the only vector for genetic sequence transfer, requiring an additional mechanism to be postulated and tested.

  136. 136
    Virgil Cain says:

    Elizabeth B Liddle- Common Descent cannot be objectively tested. No one knows if changes to DNA can account for all of the physiological and morphological changes required. You don’t have a mechanism.

    The rabbit in the Cambrian is an illusion as yours cannot account for any rabbits, anywhere.

    And yes producing and following a nested hierarchy is a perfect way to control a complex design. Network admins do it all of the time.

  137. 137
    Virgil Cain says:

    The mechanisms of evolutionism do not give rise to orderly trees. The fact that an orderly tree can be constructed should be evidence against it.

  138. 138
    Eric Anderson says:

    wd400, thanks for the clarification. Your point in bringing up Bertrand’s Paradox is simply to highlight the need for a clear example, not that Bertrand’s Paradox has any substantive impact on our ability to detect design in the typical coin H/T example.

    Fair enough. Just wanted to make sure everyone else on the thread doesn’t go down an unnecessary rabbit hole with the repeated links to Bertrand’s Paradox . . .

  139. 139
    Phinehas says:

    EL:

    That’s why the fabled rabbit-in-the-Cambrian would be such a problem. It would seriously muck up the tree predicted by common descent. As indeed the HGT signal did – and showed that longitudinal descent is not the only vector for genetic sequence transfer, requiring an additional mechanism to be postulated and tested.

    Surely the rabbit in the Cambrian would only be a temporary setback. I’m sure an additional mechanism would be postulated rather quickly and the evolution of evolution would continue unabated.

  140. 140

    Well, certainly an additional mechanism would have to be postulated. But that would then have to be tested. What sort of mechanism do you suggest? Alien rabbits? Perhaps Alien rabbitiform designers who then masterminded evolution in order to evolve Intelligent Rabbits? But who messed up at the last minute and ended up with stupid rabbits and intelligent apes instead?

    Of course new data that is unpredicted by a theory requires modification or addition to the theory, just as the behaviour of light did with Newton. That isn’t a weakness of scientific methodology – it’s its strength. Models must always be fitted to data, not the other way round. And those models must then predict new data. If they don’t, then we cannot consider them supported.

  141. 141
    Jack Jones says:

    @135 . “That’s why the fabled rabbit-in-the-Cambrian would be such a problem.”

    That example is so pathetic, it was said long after the pattern of the fossil record was already known.

    They probably would never classify such a fossil as Cambrian even if it was in such strata, if they did then they would use a term like “rabbit like” or they would invoke convergent evolution and that such a creature re evolved again much later on.

    If none of that helped then they would stack it on the shelf as an anomaly to be explained later on.

    “It would seriously muck up the tree predicted by common descent”

    No… What common descent would predict is continuity not stasis and discontinuity, the fact that we are able to have a classification system and classify organisms is because of the discontinuous nature of living things, on common descent then there would be continuums of organisms in all populations, in the middle of evolutionary change except where there was the toll of extinction.

    The nature of biology is discontinuous where your faith if you were consistent is about one of continuity.

    The fact that you can accommodate such a thing inconsistent with your faith is more down to your dogmatic need for your faith to be true than anything else.

  142. 142
    Jack Jones says:

    Or they may say what Stephen Westrop said

    “That unfalsifiable Cambrian rabbit, and sanity …
    September 13, 2013

    Further to “Top psychology mag asks if creationists are sane ,”someone reminded us this morning of something Jonathan Wells, author of The Myth of Junk DNA, has pointed out: When J.B.S. Haldane said that a fossil rabbit found in the Cambrian would prove Darwin’s theory wrong, Darwin’s followers don’t actually believe that. This was accidentally tested.

    On September 29, 2009, Dr. Stephen Westrop, Sam Noble Museum of Natural History Curator of Invertebrate Paleontology, gave a free public lecture to pre-refute a scheduled lecture by Steve Meyer at the museum later that evening on the Cambrian Explosion. Westrop concluded by taking exception to J.B.S. Haldane’s claim that finding a fossil rabbit in the pre-Cambrian would prove Darwin’s theory wrong. If such a fossil were found, Westrop said, paleontologists would simply revise their reconstruction of the history of life. During the Q&A, one student asked him whether any fossil find could falsify Darwin’s theory, and Professor Westrop said “No,” since Darwin’s theory is really about natural selection, which operates on a much shorter time scale than the fossil record.

    If finding a mammalian vertebrate fossil in the Cambrian, half a billion years ago, would prompt no serious rethink in paleontology, the belief in Darwinism is actually irrelevant to evidence from nature.

    Is that sane?”

    http://www.uncommondescent.com.....nd-sanity/

    It is pretty pathetic as the rabbit example was said long after the pattern of the fossil record was known.

    This Liddle woman is meant to be a professional and yet she uses such a sophomoric argument.

  143. 143
    kairosfocus says:

    EL:

    It’s not bias against the idea of God, it’s just a feature of scientific methodology that it can’t test unfalsifiable hypotheses.

    Really, now!

    The patent truth is that anti-theism has been institutionalised in the mindset of those inculcated with evolutionary materialist scientism.

    As well you know.

    As far as the design inference is concerned, the god of the gaps talking point and pretense that it is about the natural vs the supernatural have long since been shown to be a false dichotomy.

    We have causal factors tracing to mechanical necessity and/or chance (which can be defined and we need not play around with probability distributions to do so) and/or intelligently directed configuration (= the artificial). As in these were on record since Plato in The Laws Bk X, 2350+ years past.

    And as recently as ~ 1970, this trichotomy was the context of Monod’s Chance and Necessity. An outright famous work and book title.

    What the modern design movement has done, and what you and others of like ilk have expended every effort to rhetorically obfuscate, is to posit that there is the reasonable possibility of empirically reliable indicia of intelligently directed configuration as material causal process . . . not even requiring that there are such, just to be open to that possibility, genuinely open.

    Process, not agent responsible for process.

    (Oh, how clever objectors love to drag the focus away from testable . . . much less problematic than “falsifiable . . . and observed reliable indicia of process to wanting to debate about agents, and to then appeal to institutionalised prejudice against the supernatural. For, long since in Ari’s The Rhetoric Bk I ch 2, it was noted that our judgements when we are pleased and friendly are very different from those we make when we are pained and hostile. And from my days of dealing with foaming at the mouth communists to this, I find that atheistical agitators — never mind their professions to sweet reason and to have even cornered the market on rationality [itself a big problem] — are forever seeking to cloud what would be otherwise quite simple even almost trivially clear issues through divide, polarise and rule tactics. And at length that is exactly what the rhetoric about suspect injection of the supernatural into science, or lies about creationists in cheap tuxedos etc etc are. And I dare use the l-word. For, this means to speak in disregard to truth, in hopes of profiting by what is said or suggested being taken as true.)

    One of these is something as commonplace as what you and others manifest by typing and posting text strings to this blog. Namely, functionally specific complex organisation and associated information. A descriptive term. Something that text strings show, and the nodes-arcs pattern of a functional entity such as an ABU 6500 reel, or for that matter the units, piping, valves and instrumentation framework of a petroleum refinery.

    D/RNA manifests such FSCO/I in the cell as text strings (implying codes and language and communication systems). Functional units such as the ribosome, or the ATP synthase rotary enzyme or the bacterial flagellum show the second type, and the metabolic reaction network is similar to the third.

    Linked, is the issue of smart gated encapsulation, joined to a metabolic automaton with a von Neumann, code using, kinematic self replication facility. Which at OOL, has to be jointly explained. And the attempt to say of=h life forms reproduce so analogies to machines are flawed fails at this level, right at the root of the tree of life icon.

    Now, there is a glorified common sense principle put forth by Newton and acknowledged by Lyell and Darwin alike, vera causa. Namely that in explaining what we cannot directly observe on its traces, we ought to only revert to causal factors shown observationally to be capable of the like effect in the here and now.

    On trillions of cases in point only intelligently directed configuration has that demonstrated capability.

    But on flimsy rhetorical excuses driven by a priori ideological materialism, it is excluded . . . often by being smeared as the suspect supernatural and as unfalsifiable or the like.

    As to unfalsifiable, I think you need to distinguish the falsifiable n principle from the falsified in fact. In principle, a simple demonstration of blind chance and mechanical necessity producing FSCO/I on a reliable observational basis, would suffice. Something yu pretty well accepted several years ago when you were studying programming and intending to produce a program that would do the trick. Whatever attempt you have made has fallen foul of the usual problem of intelligence by the back door.

    And, as for the ideological bias, Rational Wiki has been pretty clear on this:

    >“Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method . . .

    I have too much respect and concern for genuine science to allow it to be ideologically redefined as applied atheism like that or the like. And you and ilk full well know that we can readily show that the above is typical, not exceptional.

    KF

  144. 144
    Zachriel says:

    John S: Every observation affirms my assumption, therefore I have proven it’s a car.

    That would be fallacy of affirming the consequent. Instead, you have supported the hypothesis. However, the claim is always considered tentative, and can be revised with new information, in this case, taking a look.

    Phinehas: If it is a tree, then isn’t it demonstrating common descent by definition?

    Trees can occur in other contexts, such as the command structure in an army.

    Phinehas: Surely the rabbit in the Cambrian would only be a temporary setback. I’m sure an additional mechanism would be postulated rather quickly and the evolution of evolution would continue unabated.

    It’s possible, but unlikely. If verified, it would precede any plausible ancestor, and would be contrary to what is known about the history of life. However, feel free to produce a rabbit in the Cambrian, and we can have that conversation.

    Elizabeth B Liddle: What sort of mechanism do you suggest? Alien rabbits?

    Time traveling rabbits. ETA: Note to self; pitch idea to HBO.

  145. 145

    One thought people might like to consider wrt to the idea that an initial “assumption” necessarily mandates a conclusion that supports it:

    Reductio ad absurdum (Latin: “reduction to absurdity”; pl.: reductiones ad absurdum), also known as argumentum ad absurdum (Latin: argument to absurdity), is a common form of argument which seeks to demonstrate that a statement is true by showing that a false, untenable, or absurd result follows from its denial, or in turn to demonstrate that a statement is false by showing that a false, untenable, or absurd result follows from its acceptance.[1]

    In other words, it doesn’t.

    That said, what is actually done in null hypothesis testing is that we formally assume the null (“there is no underlying tree pattern”) and compute how probable our results are if our null is true.

    Just as the way you infer that 500 heads were not the result of 500 fair tosses of a fair coin is by computing the probability of that result if the null (a fair coin, fairly tosses) is true.

    In both cases, if the probability is very low, you reject the null, and if the probability is high, you retain it.

  146. 146
    StephenB says:

    In cladistics, common descent is assumed to be true prior to the introduction of the evidence. If the explanation is established before the evidence speaks, then it cannot also be established after the evidence speaks. “Before” cannot also be “after.”

    Zachriel

    In hypothetico-deduction, the basis of the scientific method, the hypothesis is the tentative assumption, and entailments are deduced from the hypothesis. It takes the form if H then E.

    Cladistics does not hypothesize common descent. A hypothesis can be falsified. Cladistics does not allow common descent to be falsified. Cladistics assumes apriori that common descent is a fact.

    The hypothesis is tentatively accepted as true in order to deduce its entailments, which are then subject to verification.

    Cladistics does not accept common descent tentatively; cladistics assumes common descent unconditionally.

    For instance, if we hypothesize the Earth rotates, from the assumption of the Earth’s rotation, we can make a series of deductions, that we should observe the retardation of the pendulum near the equator. We then test that entailment to either support or falsify the hypothesis.

    Cladistics does not allow common descent to be falsified. It assumes, without qualification or condition, that common descent is true. Then it arranges the evidence to harmonize with that claim.

  147. 147

    Stephen B: “In cladistics, common descent is assumed to be true prior to the introduction of the evidence.”

    No, it isn’t. That’s why, as Nick explains, you construct a null distribution.

    In any case, an argument that goes “let us assume X is true. If our assumption is correct, we should then see Y. We do not see Y. Therefore X is not true”, is a perfectly valid argument, and does not result in confirmation of the starting assumption.

    In that context, “assumption” is used as a synonym for “hypothesis”. We allow for the possiblity that the “assumption” may be false, and test its truth against observations we would expect if it were true.

    However, the fact remains that in null hypothesis testing of phylogenetic relationships, the “assumption” i.e. the hypothesis that is tested is the null of “no tree”. So the formal starting assumption is NOT that there is an underlying tree. It is that there is not.

  148. 148
    Virgil Cain says:

    Elizabeth, There isn’t any null distribution. If Common Ancestry is true it would only produce an orderly tree under specific circumstances- ie special pleading.

    Common Ancestry remains an untestable concept and as such is not scientific regardless of whether or not it is true.

  149. 149
    Virgil Cain says:

    However, feel free to produce a rabbit in the Cambrian, and we can have that conversation.

    Feel free to tell us how evolutionism can explain the existence of rabbits.

  150. 150
    Seversky says:

    Zachriel @ 144

    Elizabeth B Liddle: What sort of mechanism do you suggest? Alien rabbits?

    Time traveling rabbits. ETA: Note to self; pitch idea to HBO.

    Great idea! Bugs Bunny for the next Dr Who – the wascally time twaveling wabbit! But instead of the rabbit in the Cambrian we find “What’s up, doc?” engraved on one of the strata.

  151. 151
    Virgil Cain says:

    If evolutionism could account for rabbits a Cambrian rabbit may have some significance. However, given that evolutionism cannot account for rabbits any discussion about rabbits is nothing but a desperate attempt at distraction and obfuscation.

  152. 152
    Jack Jones says:

    @151 “If evolutionism could account for rabbits a Cambrian rabbit may have some significance. However, given that evolutionism cannot account for rabbits any discussion about rabbits is nothing but a desperate attempt at distraction and obfuscation.”

    You’re damn right Mr Cain, They need to account for rabbits in the first place and they can’t.

    Now…We know Evolutionists deny known chemistry with their faith of life originating spontaneously and they rely on magic words when it comes to their faith in general.

    Evolutionists Explain Design Using Unscientific “Magic Words”

    “The term “magic words” is used here as a concise idiom that describes the best words evolutionists use to explain “apparent” design. Evolutionists confidently insist that a complex biological feature simply “appeared,” “emerged,” “arose,” “gave rise to,” “burst onto the scene,” “evolved itself,” “derived,” “was on the way to becoming,” “radiated into,” “modified itself,” “became a miracle of evolution,” “was making the transition to,” “manufactured itself,” “evolution’s way of dealing with,” “derived emergent properties,” or “was lucky.”

    How do words like “appeared” explain design? Just like magic, the use of this word invokes mysterious powers within unseen universes that are capable of leaping over enormous scientific obstacles without having to provide any scientific consideration for how a particular physical result was achieved. Magic words convey wish-like convictions that if evolutionists just believe deeply enough, their explanations must be true and someday will be true–though currently resisted by all scientific evidence. Explaining design by believing it “arose” appeals to imaginary special forces which help evolutionists to connect the evolutionary dots. But as in any magical kingdom, the connections are mental fantasies that are not grounded in reality.

    Magic words lack explanatory power because they fail to tie real observations to detailed descriptions of how features of design originate. Claiming that novel biological features “burst onto the scene” abandons the need for experimental verification; indeed, the implication is to not even try. Take any biological observation. In evolutionary thinking, any observation can be transformed into a proof that explains its own existence by applying the magic phrase: “It exists because it is favored by natural selection.” In reality, observations are only observations and are neither proofs nor explanations.

    Engineers, medical doctors, and other scientists who rely on studies or experiments do not use these kinds of words. Their products do not “emerge” but develop via thought-filled processes.”

    http://www.icr.org/article/unm.....gic-words/

  153. 153
    Mung says:

    Analysis and Synthesis! Back to Newton!

  154. 154
    StephenB says:

    Elizabeth Liddle

    However, the fact remains that in null hypothesis testing of phylogenetic relationships, the “assumption” i.e. the hypothesis that is tested is the null of “no tree”. So the formal starting assumption is NOT that there is an underlying tree. It is that there is not.

    No. Cladistics assumes apriori that any group of organisms is related by descent from a common ancestor. That is the starting point. Any hypothesis that follows is based on the assumption of an evolutionary relationship.

  155. 155
    Mung says:

    Lizzie, does cladistics test the null or the non null?

  156. 156
    Mung says:

    For Elizabeth, because she still doesn’t get it.

    In logic, an argument is valid if and only if it takes a form that makes it impossible for the premises to be true and the conclusion nevertheless to be false.

  157. 157

    Mung: formally, Mung, in null hypothesis testing, such as at least some forms of phylogenetic analysis such as that described by Nick Matzke, the hypothesis that it tested is the null. That is why you generate a “null distribution”.

    Mapou: Yes, I get that. Perhaps read some of my posts above for examples of why making a provisional assumption, finding out what is entailed if the assumption is true, and finding out whether those entailments are observed, allows you to draw the conclusion that your assumption is false. Your provisional assumption is in this case called a “hypothesis” as in “hypothetical”: we consider the “hypothetical” case in which the “assumption” is true.

    “Reductio ad absurdum” is an example, and is NOT fallacious.

  158. 158

    StephenB: “No. Cladistics assumes apriori that any group of organisms is related by descent from a common ancestor. That is the starting point. Any hypothesis that follows is based on the assumption of an evolutionary relationship.”

    Are you suggesting that all statistical hypothesis testing assumes the consequent?

    Or only in “cladistics”?

  159. 159

    Of course, informally, someone doing a phylogenetic analysis will “assume” in the sense of “expect” a signal of common descent, just as someone figuring out how to launch a satellite will assume the earth is spherical.

    But formally, what is tested is the null hypothesis, i.e. the provisional assumption that there is no underlying tree signal in the data, even though the investigator might take it for granted that there will be.

    Though I should point out, again, that testing a provisional assumption by finding out what would happen if it were true, and finding out whether that thing happened or not, does NOT “assume the consequent”. It is perfectly possible from such an argument to conclude that the initial provisional assumption was false.

    It’s the basic principle of falsification. People seem to be confusing “assumption” as in “hypothesis” with “assumption” as in “premise”. In the former sense, the assumption is provisional and can be shown to be false.

  160. 160
    kairosfocus says:

    EL,

    given the obvious a priori imposition of evolutionary materialist scientism, there is no effective room for serious testing of major commitments tied to that ideology.

    No wonder Johnson warned:

    For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence.

    [–> notice, the power of an undisclosed, question-begging, controlling assumption . . . often put up as if it were a mere reasonable methodological constraint; emphasis added. Let us note how Rational Wiki, so-called, presents it:

    “Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses.”

    Of course, this ideological imposition on science that subverts it from freely seeking the empirically, observationally anchored truth about our world pivots on the deception of side-stepping the obvious fact since Plato in The Laws Bk X, that there is a second, readily empirically testable and observable alternative to “natural vs [the suspect] supernatural.” Namely, blind chance and/or mechanical necessity [= the natural] vs the ART-ificial, the latter acting by evident intelligently directed configuration. [Cf Plantinga’s reply here and here.]

    And as for the god of the gaps canard, the issue is, inference to best explanation across competing live option candidates. If chance and necessity is a candidate, so is intelligence acting by art through design. And if the latter is twisted into a caricature god of the gaps strawman, then locked out, huge questions are being oh so conveniently begged.]

    That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

    To think other than such, would be naive at best.

    We need to rethink the underlying controlling assumptions at work.

    KF

  161. 161
    Bob O'H says:

    wd400 @ 100 –

    What on earth “Moral certainty” has do with any of this I can’t imagine

    Well, actually, quite a lot. Laplace used his development of what we now call Bayesian methods to look at whether the sex ratio in Paris children was 1:1. Condorcet’s summary of this is that “there is a very great probability, almost equivalent to a moral certainty that the excess of the number of births of boys has a physical cause for Paris”.

    So there you go. Busted.

  162. 162
    kairosfocus says:

    Bob O’H

    Fail.

    First, through a simple Google Search, you could easily have learned that moral certainty is a practical degree of warrant for X (typically for things not susceptible of deductive proof from generally accepted axioms) where one would be irresponsible to insist on acting as though NOT-X were true, on the balance of the relevant evidence.

    In the court room, it speaks to warrant beyond a reasonable doubt.

    Here is a Law Dictionary definition:

    moral certainty

    n. in a criminal trial, the reasonable belief (but falling short of absolute certainty) of the trier of the fact (jury or judge sitting without a jury) that the evidence shows the defendant is guilty. Moral certainty is another way of saying: “beyond a reasonable doubt.” Since there is no exact measure of certainty it is always somewhat subjective and based on “reasonable” opinions of judge and/or jury. (See: verdict, beyond a reasonable doubt)

    (n.d.) Burton’s Legal Thesaurus, 4E. (2007). Retrieved November 25 2015 from http://legal-dictionary.thefre.....+certainty

    Second, it is actually not the case that sex ratio at birth is consistently not statistically different from 1:1; here is a quick clip from Wiki:

    In a study around 2002, the natural sex ratio at birth was estimated to be close to 1.06 males/female.[7] In most populations, adult males tend to have higher death rates than adult females of the same age (even after allowing for causes specific to females such as death in childbirth), both due to natural causes such as heart attacks and strokes, which account for by far the majority of deaths and also to violent causes, such as homicide and warfare (for example, in the USA as of 2006, an adult non-elderly male is 3 to 6 times more likely to become a victim of a homicide and 2.5 to 3.5 times more likely to die in an accident than a female of the same age),[8] resulting in higher life expectancy of females. Consequently, the sex ratio tends to reduce as age increases, and among the elderly there is usually an excess of females. For example, the male to female ratio falls from 1.05 for the group aged 15 to 65 to 0.70 for the group over 65 in Germany, from 1.00 to 0.72 in the USA, from 1.06 to 0.91 in mainland China and from 1.07 to 1.02 in India.

    In the United States, the sex ratios at birth over the period 1970–2002 were 1.05 for the white non-Hispanic population, 1.04 for Mexican Americans, 1.03 for African Americans and Indians, and 1.07 for mothers of Chinese or Filipino ethnicity.[9] Among Western European countries ca. 2001, the ratios ranged from 1.04 in Belgium to 1.07 in Switzerland,[10] Italy,[11] Ireland[12] and Portugal. In the aggregated results of 56 Demographic and Health Surveys[13] in African countries, the ratio is 1.03, though there is also considerable country-to-country variation.[14]

    Even in the absence of sex selection practices, a range of “normal” sex ratios at birth of between 103 to 108 boys per 100 girls has been observed in different economically developed countries,[15] and among different ethnic and racial groups within a given country.

    In an extensive study, carried out around 2005, of sex ratio at birth in the United States from 1940 over 62 years,[16] statistical evidence suggested the following: For mothers having their first baby, the total sex ratio at birth was 1.06 overall, with some years at 1.07. For mothers having babies after the first, this ratio consistently decreased with each additional baby from 1.06 towards 1.03. The age of the mother affected the ratio: the overall ratio was 1.05 for mothers aged 25 to 35 at the time of birth; while mothers who were below the age of 15 or above 40 had babies with a sex ratio ranging between 0.94 to 1.11, and a total sex ratio of 1.04. This United States study also noted that American mothers of Hawaiian, Filipino, Chinese, Cuban and Japanese ethnicity had the highest sex ratio, with years as high as 1.14 and average sex ratio of 1.07 over the 62-year study period . . . .

    the trends in human sex ratio are not consistent across countries at a given time, or over time for a given country. In economically developed countries, as well as developing countries, these scientific studies have found that the human sex ratio at birth has historically varied between 0.94 to 1.15 for natural reasons.

    In a scientific paper published in 2008,[19] James states that conventional assumptions have been:

    there are equal numbers of X and Y chromosomes in mammalian sperm
    X and Y stand equal chance of achieving conception
    therefore equal number of male and female zygotes are formed, and that
    therefore any variation of sex ratio at birth is due to sex selection between conception and birth.

    James cautions that available scientific evidence stands against the above assumptions and conclusions. He reports that there is an excess of males at birth in almost all human populations, and the natural sex ratio at birth is usually between 1.02 to 1.08. However the ratio may deviate significantly from this range for natural reasons.

    In short it is pretty clear that human sex ratio at birth can and does vary significantly from 1:1 for various reasons.

    KF

  163. 163
    EugeneS says:

    Bob,

    “It makes specific predictions about the data (e.g. a straight line fit),which we can test.”

    Actually, if your data is rich enough, you can interpolate it using different curves of your choice: you can choose a straight line or a polynomial spline.

    Again, you test the theory but not the underlying assumptions. It is not the same.

  164. 164
    Zachriel says:

    StephenB: Cladistics assumes apriori that any group of organisms is related by descent from a common ancestor. That is the starting point. Any hypothesis that follows is based on the assumption of an evolutionary relationship.

    Cladistics is a type of analysis. While algorithms will always return a tree, they also usually return a statistical measure of fit. In addition, by using different data-sets, we can determine whether the tree is consistent. This is all within cladistics, though drawing a line between cladistics and the rest of biology has no argumentative power.

    EugeneS: Actually, if your data is rich enough, you can interpolate it using different curves of your choice: you can choose a straight line or a polynomial spline.

    Sure, and you can also calculate the statistical measure of fit to each of those curves.

    Not sure what point is being raised. There’s no doubt there is a tree-like structure for most biological traits across many taxa.

  165. 165
    Virgil Cain says:

    Cladistics is a type of analysis.

    Cladistics is a type of analysis that assumes Common Descent and then tries to make evolutionary relationships based on shared characteristics.

    There’s no doubt there is a tree-like structure for most biological traits across many taxa.

    That is expected from a Common Design.

  166. 166
    Bob O'H says:

    EugeneS @163 – We’re getting nowhere, are we? Yes, we can fit more than one curve to data. But if we fit a curve which represents a theory, then we can test that theory by checking how well that curve fits the data.

    Again, look at Anscombe’s residuals as an example of how this can be done.

  167. 167
    kairosfocus says:

    Bob O’H: kindly cf 162 above (replying to your 161) on sex ratios. KF

  168. 168
    groovamos says:

    Liddle: just as someone figuring out how to launch a satellite will assume the earth is spherical.

    Wow. Any engineer in a meeting would be laughed at for such an assumption without substantial qualification, and if not self-correcting could or would be fired.

    Same as if any engineer invoked “inverse square law” for earth’s gravitation.

    My fifth grade teacher Mrs. Woodall cleared up the “earth spherical” assumption for me to my amazement, no wonder it stuck.

    Problem is when do you ever see substantial qualification when “tree of life” is invoked in the schools. Big Problem. Not just a scientific one but more so a societal one.

  169. 169
    kairosfocus says:

    groov, there is also the conflation of an observable oblate spheroid shape with unobservables of the past of origins, and worldview impositions that then control allowed inferences and conclusions. KF

  170. 170
    Bob O'H says:

    kf @ 167 – I didn’t respond as you had obviously not even read what I had written. had you done that, you would have realised that Laplace was showing that the sex ratio at birth in Paris at the time was not 1:1.

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