Lawyers and Scientists

There’s been a skirmish between Larry Moran and Barry Arrington about whether Barry understands the Theory of Evolution, and the latest salvo is a piece at UD, entitled, Can a Lowly Lawyer Make a Useful Contribution? Maybe.

Well, in a sense, Barry makes a useful contribution in that post, as he gives a very nice illustration of a common misunderstanding about the process of hypothesis testing, in this case, basic model-fitting and null hypothesis testing, the workhorse (with all its faults) of scientific research.  Barry writes:

[Philip]Johnson is saying that attorneys are trained to detect baloney.  And that training is very helpful in the evolution debate, because that debate is chock-full of faulty logic (especially circular reasoning), abuse of language (especially equivocations), assumptions masquerading as facts, unexamined premises, etc. etc.

Consider, to take one example of many, cladistics.  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 summary, I am trained to evaluate arguments by stripping them down to examine the meaning of the terms used, exposing the underlying assumptions, and following the logic (or, as is often the case, exposing the lack of logic).  And I think I do a pretty fair job of that, both in my legal practice and here at UD.

Barry has made two common errors here.  First he has confused the assumption of common descent with the conclusion of common descent, and thus detected circular reasoning where there is none.  Secondly he has confused the process of fitting a model with the broader concept of a hypothesised model.

To take a simpler example, but one that is directly analogous.  Suppose we hypothesis a correlation between, say,  Body Mass Index and lifespan.  We theorise that the higher your body mass, the more vulnerable you are to various pathological process, and therefore the more likely you are to die young – in other words we hypothesis a broadly monotonic relationship betwen BMI and age at death.  The traditional way of doing this is to get a sample data, find the best-fit line for BMI against age at death, and test the null hypothesis that the “best fit line” in the population from which we drew our sample would have a slope of zero.  It’s a stupid null, in fact, because the null, expressed thus, is always false – no slope is ever exactly zero.  But because data are noisy (skinny people die young for lots of reasons and sometimes obese people live to a ripe old age, also for lots of reasons) it’s still a good test value – if we can show that our actual fitted line, under the null, is unlikely to to be found in a sample drawn from a population that has a slope of zero, then we can reject the null that there is no linear relationship in the population, even though we may be not entitled to reject a different null that there is a smaller one than the one our data seem to indicate.

My first point being that we start off by making a prediction, based on theory.  We then propose a model, based on that theory: that there will be a roughly linear relationship between BMI and age-at-death.  Choosing to fit a linear model does not entail the assumption that there is a linear relationship, because we actually test the null that there is NO linear relationship.  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”.

Going back to the linear slope example: as our null is that the true best-fit line in the is zero, a slope of more than a certain slope-iness, whether positive or negative, will require us to reject that null, even though our theory predicts a negative slope (higher BMI associated with lower age at death).  So a confident rejection of our null doesn not necessarily support our theory, nor accord with our prediction – it allows us to get a surprise: maybe all those fries and donuts are actually helping us live longer!  This is why, while we may privately (or publicly) predict a negative slope, because that is what our theory leads us to expect if true, we have to allow for a fitted slope that not only indicates that our null is false but that our theory is false too.

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 (just as when I fit a linear model to the BMI/age at death data, I am testing the null that there is no linear slope), but she is also finding out what the tree, if there is one, actually is, and may be surprised (just as when I fit a linear model to the BMI/age at deat data, I may find my fitted model is positive, not negative).

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.  It’s what Linnaeus found, it’s what YECs need to get their animals on to the ark, and the only fundamental disputes are whether there is one tree or several.  So a tree is a good basic model, and is the workhorse model for palaentology just as the linear model underlies most research in social and health sciences (indeed, it’s called the General Linear Model, GLM to its friends)  Nonetheless, we need to be aware that there are potential other models (non-linear; non-tree) that might fit better. But trees fit pretty damn well for palaeontological data.

They are, instead, interested in the model fit.  Just as by now we don’t really have to test the basic hypothesis that BMI is negatively correlated with health, but rather want to find out HOW much it correlates with different aspects of health, and just how many years an extra donut will knock of our expected span.  And, directly analagously, that’s what the palaeontologist does – she wants to know whether the best fitting model supports this, or that, idea about which organisms branched off from which other organisms, when.

So, Barry: yes, you’ve helped, by articulating precisely the problem so many people have in understanding how quantitative models are tested in science. So let me summarise:

  • The reasoning is not circular, because we test the null, not the hypothesis – we do not assume our hypothesis is true, rather we figure out how likely our data are to be as extreme as they are if our hypothesis is false.  Dembski is good on this, btw.
  • There is a different between choosing a model and fitting a model.  We choose a tree, or a slope,model because we want to test the null that there is no tree or no slope.  However, when we FIT the model, we make no prior assumptions about the degree or direction of fit.  And we are often much more interested in the parameters of the fit (which tree, what slope) than whether there is in fact a tree/slope.  That’s important, but it’s neither assumed nor imposed.

 

50 thoughts on “Lawyers and Scientists

  1. I know the term gets thrown around a lot as a pejorative but Barry Arrington really could be the poster boy for Dunning-Kruger syndrome.

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

    Of course it does. What a ridiculously ignorant dweeb.

    I don’t dispute that cladistics assumes common descent, as that had been well-established before cladistics was worked out. Nevertheless, it would take almost no time at all for cladistics to utterly fail at classifying automobiles according to common descent, hence falsifying the hypothesis that automobiles arise via common descent. Likewise with organisms, if they did not typically reveal the expectations of common descent (HGT is a known exception–and even organisms undergoing that process essentially reveal common descent in certain fundamental genes), it would be very easily recognized that life didn’t conform to the assumption of common descent.

    Cladistics cannot work with known designed objects, in other words. It only works if life arises by common descent, and without substantial input from poofs.

    Glen Davidson

  3. Well, it certainly looks like prima facie evidence that Barry doesn’t, in fact, understand the Theory of Evolution, or how it is tested, at any rate.

  4. What Arrington seems to not understand is — not surprisingly — how science is done. Although cladistics takes shared ancestry as a background assumption, it also tests that assumption by seeing if the data generates consistent patterns.

    Apart from long-standing and insoluble worries about how all data is theory-laden, there is nothing circular about how we arrive at hypotheses, test them against data, and revise them as needed.

    If you try and squeeze the structure of scientific explanation into the deductive structure of argument, then yes, it will look circular. But the appearance of circularity is generated by neglecting the fundamental difference between explanations and arguments.

    It might be that, at the end of the day, all there is to ID rests on this elementary conflation.

  5. Elizabeth,

    You believe there is a theory of modern medicine. You also believe that theories don’t need to be falsifiable, nor specific, or unambiguous. You also believe you understand biology better than Cornelius Hunter.

    So you should probably be a bit careful about your criticisms of Barry.

  6. Kantian Naturalist,

    When someone tries to say how “science is done” one should already be suspect about their conclusion. Science isn’t done any one way. Science is simply a search for reality. Its done any way one wants.

    Skeptics try to own the concept of the scientific process. No such process exists. We search, we find. That is science.

  7. phoodoo:
    Elizabeth,

    You believe there is a theory of modern medicine.You also believe that theories don’t need to be falsifiable, nor specific, or unambiguous. You also believe you understand biology better than Cornelius Hunter.

    The stuff I scrape off the bottom of my shoe understands biology better than Cornelius Hunter.

  8. Barry:

    Back to our cladistics example. I have a very general understanding of how clads are made and what they mean.

    LOL.

  9. Evolutionary theory should not be held up as a model of science.

    In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to [the pseudo science of] phrenology than to physics.

    Similarity implies common descent even though in many cases it doesn’t make sense and we have to fill the gaps with convergence, which sort of means we don’t really need to assume common descent as an explanation any way, but evolutionary theorists will anyway.

    No matter that some of the transformations proposed make little sense from a mechanical standpoint and that natural selection as actually seen observationally doesn’t work as advertised ( elimination of species and complexity via means of natural selection, not creation of it).

    Histones, spliceosomal introns sort of appear without much of an explanation mechanically, but without a plausible model of why their emergence is reasonable (from some undefined precoursor) it is accepted as fact. What we call such lines of reasoning are non-sequiturs. The conclusions do not follow from the premises.

    I could list a few proteins associated with histone modification:

    histone acetyl transferase
    histone deacetyl transferase
    histones themselves

    how and why did they emerge? Evolutionary theory assumes they evolved — which isn’t much of theory beyond “it happened”.

    A real scientific theory would be the approximations of Newtonian mechanics, that although are an approximation, for most every day physics (including lots of atomic physics) it’s pretty powerful. Even the special case of

    F = 0

    is used in a lot of building construction as it states the fundamental concept of “statics”.

    I’m personally sorry I’ve wasted so much time learning about a theory that’s at the bottom of science’s pecking order rather than learning basic science like organic chemistry.

  10. stcordova:

    I’m personally sorry I’ve wasted so much time learning about a theory that’s at the bottom of science’s pecking order rather than learning basic science like organic chemistry.

    Based on this latest Gish Gallop of misunderstandings and Creationist hooey I’d say you didn’t learn anything about actual evolutionary theory at all.

  11. BTW Sal, your quote-mined quote from Jerry Coyne was the usual Creationist garbage. Here is the whole quote in context.

    Coyne: “In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history’s inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike “harder” scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture.”

    It’s the opening paragraph of a Coyne critique of a book on evolutionary psychology.

    Of Vice and Men: The fairy tales of evolutionary psychology.

    Of course in context Coyne isn’t saying anything close to the picture you paint. But you already knew that.

  12. stcordova,

    Very well put. One of your best posts in my opinion.

    The “it just happened” aspect of evolutionary thought is just so void of any desire to contemplate the deeper problem. One can not help but be persuaded that so many of these people did not want to think about it. Its too inconvenient, and yet that mindset exists at such high levels of academia.

    Its astounding to me.

  13. phoodoo,

    You also believe you understand biology better than Cornelius Hunter.

    It is a pretty safe bet that there is somebody in the world who understands biology better than Cornelius Hunter. It is also a safe bet that that somebody (those somebodies) is (are) an ‘evolutionist (s)’. So I’m not sure where that argument from authority, or lack thereof, is supposed to take us.

  14. phoodoo: The “it just happened” aspect of evolutionary thought is just so void of any desire to contemplate the deeper problem.

    Yes, I personally find “it was designed” to be much more intellectually satisfying.

  15. Consider, to take one example of many, cladistics. It does not take a genius to know that cladistic techniques do not establish common descent; rather they assume it.

    My favourite argument on this relates to paternity testing – something that lawyers may twist and turn to either prove or disprove. It is equally applicable to forensic DNA testing.

    Such legally admissible tests rest upon an assumption of common descent – not that this DNA is definitively commonly descended with that, but what would we expect to see if it was vs if it wasn’t? So if you deny cladistics on the ‘circular’ argument, you must also throw out all evidence of genetic relatedness of individuals, and of forensic samples to victim/defendant. What say you, Legal Eagle?

  16. stcordova: I’m personally sorry I’ve wasted so much time learning about a theory that’s at the bottom of science’s pecking order rather than learning basic science like organic chemistry.

    But you haven’t! You’ve not studied biology formally, you’ve published nothing and you think your misunderstandings are actually insights. Try publishing something, see how far you get. But silly me, the Darwinist cabal would of course prevent anything critical being published, so best not to bother eh?

  17. Allan Miller: My favourite argument on this relates to paternity testing – something that lawyers may twist and turn to either prove or disprove. It is equally applicable to forensic DNA testing.

    Such legally admissible tests rest upon an assumption of common descent – not that this DNA is definitively commonly descended with that, but what would we expect to see if it was vs if it wasn’t? So if you deny cladistics on the ‘circular’ argument, you must also throw out all evidence of genetic relatedness of individuals, and of forensic samples to victim/defendant. What say you, Legal Eagle?

    We don’t even have to use DNA paternity testing here.
    Presumably Stcordova would think something was amiss if his wife gave birth to african american children. Surely they can’t be related to him?

  18. petrushka:
    Sal could submit his writings to BioComplexity.

    I think you’ll find the Darwinist cabal controls that also. Otherwise I’m sure Upright Biped and KF would already have published there.

  19. phoodoo: I am sure your book will be out any day now.

    Heh, it’s telling that you think science is advanced by books rather then publishing of peer reviewed papers.

    phoodoo: Hypocrisy is your greatest weapon.

    You tell me why KF, UB and Sal refuse to publish their work in a place where it can be critiqued on the record and where other scientists might actually read it .

  20. OMagain: I think you’ll find the Darwinist cabal controls that also.

    The cabal successfuly nixed the entire journal.

    Home > Current > Vol 2014

    Despite:

    BIO-Complexity welcomes a new editor in Chief

    The editors of BIO-Complexity welcome Professor Robert J. Marks II as the journal’s second Editor in Chief. Dr. Marks has been an active member of the editorial board since the journal’s launch, co-authoring four BIO-Complexity papers in that time, in addition to his other editorial duties. We look forward to the next five years!

    Posted: 2015-06-05

  21. IDiot-creationists have gradually manipulated many people into using the words intelligent design, design, designed, the designer, intelligent agent, intelligent being, ID advocate, IDist, ID proponent, etc., instead of created, creation, specially created, creator, Allah, God, Jesus, Holy Ghost, Satan, angels, demons, creationist, etc.

    Think about it.

  22. Sal refuse to publish their work in a place where it can be critiqued on the record and where other scientists might actually read it .

    Hey, I’m publishing here at the illustrious venue known as TSZ. 🙂

    Anyone want to go on the record about Histone modifications (a new code). How about these modifications that are getting discovered that affect the epitranscriptome. How the heck did they evolve the machines (like say RNA methyltransferases)?

    http://modomics.genesilico.pl/modifications/

    Look at page 7 of this document, namely the tRNA epitranscriptomic modifications.

    https://dpcpsi.nih.gov/sites/default/files/council%20jan%2030%202015%20Pres%20E4.pdf

    Where did the machinery emerge to manage those eiptrancriptome modifications? Oh, I know, “evolution did it, that settles it.” That’s about the extent of what it means to understand evolutionary theory.
    Even parrot could almost say, “Evolution did it.”

    I don’t worry about Larry Moran and Dan Graur. Francis Collins is putting his money where his mouth isn’t, on exploring JunkDNA. To the tune of 600 million dollars:

    ENCODE : about 200 million
    Roadmap: about 200 million
    E4: about 200 million

    ” If ENCODE is right, then Evolution is wrong.” Dan Graur.

    There is a 600 million dollar bet by the NIH that ENCODE is right.

  23. stcordova: Hey, I’m publishing here at the illustrious venue known as TSZ.

    If you say so. It’s obvious to all you have no confidence in your ideas, yet strangly keep talking about them.

    stcordova: Where did the machinery emerge to manage those eiptrancriptome modifications? Oh, I know, “evolution did it, that settles it.” That’s about the extent of what it means to understand evolutionary theory.
    Even parrot could almost say, “Evolution did it.”

    No, that’s what you think people would do because that’s exactly what you would do yourself in the same situation. Except you’d say “the designer did it”.

    But luckily for us all, there are people out there with the courage of their convictions.

  24. stcordova: Anyone want to go on the record about Histone modifications (a new code). How about these modifications that are getting discovered that affect the epitranscriptome. How the heck did they evolve the machines (like say RNA methyltransferases)?

    Submit a grant proposal if you are so interested. Or just assume the designer did it, and move on.

  25. Sal’s is such a typical response to evidence.

    The cladistic evidence for evolution is presented, the fact that known designed objects do not conform to a cladistic pattern is pointed out, and what does he do? Bring in an alternate explanation (beyond “Designer wanted it that way,” or equivalent), actually consider what the evidence indicates, or muster any real curiosity about the phenomena at all? Of course not, it’s the same dreary “throw shit at it” response that one always gets from IDiots.

    We know there are questions. That’s a lot of the point of having a real explanation, problems are thereby possible–and a way to discover solutions is opened. IDiocy has no problems, because it has no explanation and no way to finding any solutions. We get that. It’s not a strength, it’s how it happens to be utterly useless drivel of no consequence except for its use as religious apologetics.

    Glen Davidson

  26. GlenDavidson: utterly useless drivel of no consequence

    That is the real problem wit ID. It is useless. It produces no research and no ideas for research.

    Come on, Sal, bless us with some research projects or designs for research.

  27. I remember that Barry periodically feels that he has to tout how his skills as a lawyer enable him to see logical flaws in other’s arguments. He is confusing winning arguments in the sense of convincing a jury or judge (which he may or may not be good at, I have no idea) with winning arguments in the sense of proving that you are correct. Lawyers have a poor track record with statistics – to the extent that there is at least one known fallacy named after them.

  28. stcordova,

    Even parrot could almost say, “Evolution did it.”

    Do you think it a sensible challenge to look at System X and demand how it evolved, else (somehow) Creationism wins? ad absurdum, until we know every detail about the evolution of everything, evolution can never be preferred to Creationism – despite that being, puzzlingly, not held to any standard of evidence whatsoever.

  29. To be fair, any set of data input to a phylogenetic analysis program will produce a tree (or sometimes several). So just seeing a tree doesn’t mean the data actually fit a tree model. But of course we have a great many ways of testing the fit of data to model, the simplest and most widely used of which is the nonparametric bootstrap. If your tree comes out with high bootstrap numbers for most of its branches (and if various other assumptions of the model are met), you can be confident that the data do indeed have a good fit to a tree model (and to that tree in particular). We do test these things, you know.

  30. I see Barry now states:

    Common descent is not necessarily false.

    I’m pleased to see Barry adopting the party line as expressed by Michael Behe. Larry Moran helpfully quotes Behe in The Edge of Evolution

    The bottom line is this. Common descent is true; yet the explanation of common descent—even the common descent of humans and chimps—although fascinating, is in a profound sense trivial. It says merely that commonalities were there from the start, present in a common ancestor. It does not even begin to explain where those commonalities came from, or how humans subsequently acquired remarkable differences. Something that is nonrandom must account for the common descent of life.

    Behe sets out the challenge for ID “theorists” to explain common descent, not to reject it.

  31. Richardthughes

    Yes, and he shows what a lawyer can do in this area, which is to badly misquote Nick Matzke to say something that looks as if it denies that phylogenetic analysis can tell us about evolutionary relationships, when all he was saying was that it doesn’t provide us with direct-ancestor relationships. The latter of which any person moderately knowledgeable in biology should already know, or at least suspect.

    Barry makes a false claim and misquotes Nick thusly:

    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.

    What Nick really wrote:

    Yet another confusion that Meyer exhibits relates to the idea of “ancestor”. As with all creationists, Meyer exhibits no understanding of the fact that phylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry, and, crucially, that this is neither a significant flaw, nor any sort of challenge to common ancestry, nor any sort of evidence against evolution. Distinguishing between a close sister-group relationship and an exact ancestor is just a level of precision that we cannot expect in most cases. It’s just a by-product of the method and the data available. (This is not quite the end of the discussion on this topic – eventually, we will have Bayesian methods that will assign probabilities to hypotheses of direct ancestry, although this will require formal definition and then data-informed estimation of what “ancestral lineage” means in terms of morphological variability within a lineage, the biogeographic and stratigraphic range of “morphospecies” through times, etc. End nerdy sidetrack.) But phylogenetic methods can and do regularly and rigorously identify collateral ancestry – sister group relationships, and ancestral grades and clades. We can say that birds descend from dinosaurs with essentially 100% statistical confidence, without knowing which if any currently-described fossils are exact direct ancestors rather than closely-related sister groups.

    http://pandasthumb.org/archives/2013/06/meyers-hopeless-2.html

    Not only is it not a challenge to evolution, it’s the expected confirmation of evolutionary relationships when using cladistics properly.

    The rest of Barry’s tripe is also pretty useless to misleading (specifically with respect to this–also generally), but this is an egregious quotemine and misuse of ellipses to make Nick out to say what he most certainly did not.

    Glen Davidson

  32. Alan Fox: It says merely that commonalities were there from the start, present in a common ancestor.

    I wonder if Behe ever walked that thought back to its inevitable conclusion.

  33. petrushka: I wonder if Behe ever walked that thought back to its inevitable conclusion.

    I think he has, which is why he accepts common descent.

    What he hasn’t done is to ask how we can ever establish that a designer would have merely tweaked life over billions of years, keeping various commonalities while generally following cladistic patterning–as in, why don’t later “designs” become common to all life, or at least to all life that could benefit from these? IOW, isn’t there something actually wrong with a design process that doesn’t produce marked differences from the entailments of evolutionary theory? Firstly, I would think that would be a major point of design, secondly, why would any designer follow the stifling constraints of unintelligent evolution, and thirdly, it’s really shitty science to claim that your great discovery of intelligent manipulation of life produces results that are indistinguishable from that of unintelligent evolution (unless through probabilities).

    Behe accepts the evidence for evolution by unintelligent means (massively derivative, etc.) as if it applies to evolution by highly intelligent means. Does he simply not think, or is he actually unable to think this through?

    Glen Davidson

  34. bFast comments:

    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.

    Which would be telling, were it not completely ignorant nonsense.

    Glen Davidson

  35. I see that Barry still doesn’t understand the difference between hypothesising a general model (linear, tree) and fitting the model (slope; nodes, branches).

    Nor between assuming your model is true (the relationship is linear; the distribution is a tree) and testing it (by seeing whether the best FIT is better than the null).

    Hasn’t even bothered to address it.

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