Before reading this, or if you have already read it, please note a third update here and a fourth one here.
A few days ago, Cdesign proponentsist JoeG challenged me to a $10,000 bet over which one of us understands the concept of nested hierarchies better. I accepted his challenge and won and he decided to chicken out and lie about the bet.
Let me recapitulate. Joe G. made a number of claims (and posted many links to sources he doesn´t understand, which in his opinion supports his ideas). Let´s start at the beginning. our disagreement started with Joe G´s claims that “everything could be placed into nested hierarchies”, that evolution from a common ancestor does not predict a nested hierarchy of similarities because “with gradual evolution we would expect to see a smooth blending of defining traits” and that the existence of transitional form demonstrates that a classification of organisms cannot correspond to a nested hierarchy because “if you have a mix of traits then a nested hierarchy is violated”.
His precise claims were:
1.
An Army is a nested hiearchy [sic]. Just about anything can be placed into a nested hierarchy. However with gradual evolution we would expect to see a smooth blending of deining [sic] traits, and that would ruin a nested hierarchy based on traits.
2.
And I am correct- transitional forms, by their very nature, contain a MIX of defining characteristics. THAT violates a nested hierarchy. Obvioulsy [sic] you don’t know anything about nested hierarchies and you think that your ignorance refutes me.
If you have a mix of traits then a nested hierarchy is violated. period. End of story.
3.
Then there is the FACT that prokaryotes do NOT fit into a strict nested hierarchy.
Geez Dr Denton went over that in “Evolution: A Theory in Crisis.
….
that is obvious by the total lack of nested hierarchy wrt prokaryotes.
While he made these claims, he challenged me to the following bet: I will put up $10,000 US to prove that I understand nested hierarchies better than you. . Which I obviously accepted, given how transparently and spectacularly wrong he was.
So I explained how he was wrong about claim Nr. 1, that “everything could be placed into a nested hierarchy”. His claim is true to the degree that software for phylogeny inference (or other software that classifies data in a hierarchical way) will return a hierarchy, no matter what the data looks like (with some exceptions, datasets where all elements are identical or completely dissimilar cannot be classified hierarchically). However, whether a dataset can be objectively assigned to a nested hierarchy is a different question, and one that can be answered using mathematical measurements of hierarchical structure coupled with associated test statistics (a frequently used measurement in this context is the consistency index). Datasets could be significantly hierarchical, anti-hierarchical, or anything in between. Phylogenetic classifications happen to correspond to statistically highly significant hierarchical structures (for an elaborate discussion see Talk Origins) while this is usually not true for “designed” objects. I gave the examples of cars, watches, cell phones and computers. For these objects, technological innovations (like navigation systems or airbags for cars) can and are routinely included in almost all models that are still sold. Their presence in a model thus usually reflects the date when the car was manufactured or the price of the car, and can not be explained by relationships like “common manufacturer / designer”, “common inspiration” or anything like that.
I´ll get to the “with gradual evolution we would expect to see a smooth blending of defining traits” claim (which is surprisingly not completely wrong) later, because it can be nicely discussed together with one of his follow-up claims.
On to claim Nr. 2. This one is not only wrong, it is as wrong a statement as one could possibly make about nested hierarchies. As I explained to him, his misconceptions, if true, would prove that nested hierarchies (or any kind of hierarchical classification for that matter) are a logical impossibility!
He claimed that “mixing traits would ruin a nested hierarchy”, but the only entities for which there is no mixing of traits / features / characters whatsoever, are entities that are identical or totally dissimilar! However, a hierarchical classification for identical or completely dissimilar objects doesn´t even make sense, because you would have objects that all have the same similarity to each other (which would be 1 and 0 respectively on a scale where 1 represents that ALL features are shared and 0 that NO features are shared). So, if no mixing of traits is ever allowed, a hierarchical classification is a logical impossibility!
For a classification like a phylogenetic tree, traits are of course shared between different organisms, but not arbitrarily. For such a tree, the distribution of traits should be explained by the relationship of a node to it´s parent node as much as possible, if these relationships explain 100% of the variation in traits and all traits emerge just once, then the consistency index I mentioned above would be maximal (=1) and the tree would correspond to a perfectly hierarchical structure. What reduces the degree of hierarchical structure are things like the multiple independent emergence of traits (convergent evolution) and horizontal gene transfer (transfer of genetic material from one organism to another that is not it´s offspring).
Regarding, transitional forms, JoeG seems to be unable to understand that those show transitions between an ancestral form and that of it´s descendants and do not represent a mix of traits from distinct groups on the same level of classification. Meaning that they obviously do not “ruin” a nested hierarchy.
Claim Nr. 3 was addressed as well – horizontal gene transfer (which is very widespread among many prokaryotes) indeed does reduce the degree of hierarchical structure for phylogenies, but since vertical transfer of genetic material is still more common than horizontal and since „hierarchical structure“ is not a binary attribute (something which Joe G. had a very hard time understanding…), prokaryotic phylogenies still have a highly significant hierarchical structure (see here and here for example).
So, JoeG was as wrong as he could possibly be and obviously (since we are dealing with a Cdesign proponentsists here) did not admit that, but rather chose to ignore the bullshit he wrote and make new claims – that a phylogenetic tree does not correspond to a nested hierarchy, that evolution doesn´t even predict a nested hierarchy and that Charles Darwin himself supports his IDiotic ideas.
His claims were:
4. A quote from a 1998 paper by Eric Knox:
The fact that speciation ends with two species, not two halves of a species, is an indication that this hierarchy lacks summativity, and therefore, is non-nested.
– with the attempt to demonstrate that phylogenetic trees are not nested hierarchies. Source.
5.
First things first- Linnean taxonomy, ie the observed nested hierarchy with animals, has nothing to do with evolution, guided or unguided. It was created to exemplify a common design. Evolutionists stole it, changed the headings and said theirs can also explain it. Note- NOT predict it, explain it.
6. A quotes from chapter 14 of “On the Origin of Species”:
Extinction has only defined the groups: it has by no means made them; for if every form which has ever lived on this earth were suddenly to reappear, though it would be quite impossible to give definitions by which each group could be distinguished, still a natural classification, or at least a natural arrangement, would be possible
Preceded by JoeG claiming “However, Darwin agrees with me.”
Source.
Note how his comments evolved and how he no longer claims most of the bullshit from the previous three claims (without acknowledging that he was wrong of course). On to his new bullshit:
Claim 4: he is not completely wrong about the Knox paper. Knox is trying to refine the terminology in systematics and distinguish between “nested”, “semi-nested” and “non-nested” hierarchies in classification, based on what “nested” exactly means in the respective context.
A classifcation where the sum of all parts at one level of organization is equal to (or rather “fully encompassed in”) the higher level of classification, would be “fully nested”, while a classification where one level of classifcation is encompassed in the next higher level, but not equal to it (because the next higher level is more general) would be “semi-nested”. And finally, a classification where the entities at one level of classification are more than the next higher level of classification (i.e. not fully encompassed by the next higher level of classification) would be non-nested.
Which effectively means that he would refer to a phylogenetic tree as “non-nested”, to a cladogram as “semi-nested” and to a structure as he shows in figure 5 as “fully-nested”. It has to be pointed out though, that there is an extreme amount of nitpicking involved in this distinction and it is not established and in practice virtually never used. And, more importantly, since most phylogenetic trees (all that would be relevant for our disagreement) can trivially be converted to a cladogram and to a structure as he shows in figure 5 (without loosing any information that would be relevant for this discussion – all that is lost is an explicit representation of time) and since this would make no difference whatsoever for our disagreement (the degree of hierarchical structure could be measured for all three and would yield the exact same result) – this supports JoeG´s claims in no way shape or form. Especially considering that he had no clue about what he was even reading because this is the claim he tried to support by citing the paper:
The point is that I had claimed that transitional forms, by their very definition, would violate a nested hierarchy scheme. Ya see they have a mix of characteristics of two or more other species, and that means you would have to create a new set, which means redefining all the old sets.
The paper has literally nothing to do with this claim whatsoever.
Claim 5:
Evolution did not predict a nested hierarchy? Of course it did. Let´s look at chaper 14 of the sixth edition of !On the Origin of Species“!(and the only figure in this book):
I request the reader to turn to the diagram illustrating the action, as formerly explained, of these several principles; and he will see that the inevitable result is, that the modified descendants proceeding from one progenitor become broken up into groups subordinate to groups. In the diagram each letter on the uppermost line may represent a genus including several species; and the whole of the genera along this upper line form together one class, for all are descended from one ancient parent, and, consequently, have inherited something in common. But the three genera on the left hand have, on this same principle, much in common, and form a subfamily, distinct from that containing the next two genera on the right hand, which diverged from a common parent at the fifth stage of descent. These five genera have also much in common, though less than when grouped in subfamilies; and they form a family distinct from that containing the three genera still further to the right hand, which diverged at an earlier period. And all these genera, descended from (A), form an order distinct from the genera descended from (I). So that we here have many species descended from a single progenitor grouped into genera; and the genera into subfamilies, families and orders, all under one great class. The grand fact of the natural subordination of organic beings in groups under groups, which, from its familiarity, does not always sufficiently strike us, is in my judgment thus explained. No doubt organic beings, like all other objects, can be classed in many ways, either artificially by single characters, or more naturally by a number of characters. We know, for instance, that minerals and the elemental substances can be thus arranged. In this case there is of course no relation to genealogical succession, and no cause can at present be assigned for their falling into groups. But with organic beings the case is different, and the view above given accords with their natural arrangement in group under group; and no other explanation has ever been attempted.
So, JoeG was wrong again. What a surprise…
Finally Claim 6 (and partly claim 1 as well):
What Darwin tried to communicate in this quote was, that demarcation criteria between groups of related organisms have been created by extinction. Think about it, if we assume that all organisms are descendants of a shared common ancestor and modifications happened gradually – how would we classify organisms if every organism that ever lived were still alive today?
There would only be one meaningful classification, one group that encompasses all life, because there would be smooth gradual transitions from every form to a closely related form. That´s what we would get with universal common descent + gradualism + ubiquitous immortality. We could still arrange species by similarity within ONE group that encompasses all life, but objective distinctions between different groups (or any form of hierarchical classification) would be impossible.
I still have no clue why JoeG thinks that this supports any of his arguments in any way, shape or form however since he must have noticed that organisms are in fact not immortal and that the overwhelming majority of all species that ever lived are extinct.
Joe G. owes me $10,000. And instead of putting his money where his mouth his, he rather lies about the matter. I offered to have this matter settled by judges and even granted him to choose the judges:
Btw, maybe you didn´t get it, but I accepted your challenge.
We could also have this settled by judges if you prefer. And, since I´m absolutely confident that I am right and you are as wrong as you could possibly be (since your hilarious misconceptions about nested hierarchies are so ridiculous that they would demonstrate that nested hierarchies are a logical impossibility if they were accurate), I let you choose the judges. Hell, they could even be Cdesign proponentsists for all I care.
All that matters to me is that they can speak with authority about the matter – professional Mathematicians (or Computer Scientists) working on classification / clustering problems, Mathematicians working on Markovian processes, Biomathematicians, Bioinformaticians working on phylogeny inference and / or Markov models, Taxonomists etc. – and that they are willing to go on the record with their name and professional affiliation (and thus risking their reputation should they lie about the subject).
Maybe JoeG is just too stupid to understand (or look up) the words and phrases “judges”, “qualified” and “go on the record”, but this is what he made out of it:
Oops. Andy sez I can use any judges I want. Well Andy I will take Darwin and Denton.
You lose.
A dead man who can´t tell Joe G. that he doesn´t understand his writings and his interpretation of a book written by a Biochemist with no training in and no contributions to the subjects we are talking about… You can´t make this shit up.
So, brave Sir Joe did not put his money where his big fat mouth is and ran away instead, who would have guessed?
[UPDATE –
Unless I missed it, it seems like there is a rather obvious flaw with Joe G’s arguments that even a non-scientist should be able to note, yet no one has pointed it out.
Joe G claimed that “everything could be placed into nested hierarchies.” However, he also says that evolution does not predict nested hierarchies, and that transitional species destroy nested hierarchies. He also said things about prokaryotes don’t fit into the nested hierarchies either. But these statements are direct contradictions: anything can be placed into such a hierarchy, and there are biological trees that cannot be put into such hierarchies. So never mind the technicalities, Joe G doesn’t even have a coherent idea to stand against the facts.
Now, being an honest person, I don’t make shit up about things I don’t know about. However, I at least know rule #1 about bullshitting: keep your story straight. So not only is Joe G a bullshitter, he isn’t even good at it.
Aaron Adair, below]
[UPDATE 2:
Joe G. has an amazing ability to repeat the same Bullshit over and over and over again without ever actually addressing the explanations and refutations he is replying to. On his blog, he claims that Douglas Theobald (of Talk Origins fame) agrees with him, he quotes Theobald´s Talk Origins essay on nested hierarchies:
It would be very problematic if many species were found that combined characteristics of different nested groupings. Proceeding with the previous example, some nonvascular plants could have seeds or flowers, like vascular plants, but they do not. Gymnosperms (e.g. conifers or pines) occasionally could be found with flowers, but they never are. Non-seed plants, like ferns, could be found with woody stems; however, only some angiosperms have woody stems. Conceivably, some birds could have mammary glands or hair; some mammals could have feathers (they are an excellent means of insulation). Certain fish or amphibians could have differentiated or cusped teeth, but these are only characteristics of mammals. A mix and match of characters like this would make it extremely difficult to objectively organize species into nested hierarchies. Unlike organisms, cars do have a mix and match of characters, and this is precisely why a nested hierarchy does not flow naturally from classification of cars.
If it were impossible, or very problematic, to place species in an objective nested classification scheme (as it is for the car, chair, book, atomic element, and elementary particle examples mentioned above), macroevolution would be effectively disproven. More precisely, if the phylogenetic tree of all life gave statistically significant low values of phylogenetic signal (hierarchical structure), common descent would be resolutely falsified.
And he thinks that this supports his Bullshit IDeas in any way, shape or form. The funny thing is that he made the exact same idiotic claim three days ago and it was already refuted by me:
No, he doesn´t [support your ideas] Genius, Theobald says:
“It would be very problematic if many species were found that combined characteristics of different nested groupings.”
=> Note that he is talking about extant species with combined characteristics of different nested groups and not about transitional forms (because those show transitions between an ancestral form and it´s descendants. Also, note that he is talking about “many”, which means that those characteristics must have emerged “many” times independently (homoplasy).And now, go back to my earlier comment, read it again, and note where I say:
“Which means that the distribution of features in the leaves should be explained as much as possible by their relationship to their parent nodes (if the relation to parent nodes explains 100% of the variation in features at the leaves and all features emerge just once (Hint: all features that DO exist actually must emerge somewhere at least one time…), the consistency index would be 1). What reduces the degree of hierarchical structure is the independent (i.e. not explainable by relation to parent node) emergence of features.“
=> You really should work on your reading comprehension. And if you were not lying about having attended college level Biology courses – print out this exchange and ask for a refund on your tuition fees.
So, he´s repeating the exact same Bullshit, pretends he wasn´t already refuted (his IDiotic misconceptions do not even need a refutation, reading comprehension would be all that is required) and he still doesn´t understand what a transitional form is (and he seems to be incapable of grasping the difference between the words “bold” / “bald” and “boldly” / “baldly”…).]
[UPDATE 3 –
Joe. G continues to show off his amazing ignorance at his blog. It´s amazing how much his answers evolve as he keeps frantically googling stuff (note how he has completely given up on his earliest bullshit claims – he´s making it up as he goes along).
Joe:
But anyway, as I told Andy, nested hierarchies are constructed by making sets. Those are specified, well-defined sets in a specified well-defined order. The more characters you can use to define your sets, the better for your nested hierarchy.
That is complete bullshit. The only thing that counts is that the variation in the lower levels of the classification is explained by them being nested in the next higher level of classification (in evolutionary terms, this translated to variation between organisms being explained by their ancestry).
What reduces the degree to which living species and their ancestors can be modelled by a nested hierarchy, is variation that cannot be explained by nodes being nested in the next higher level of classification (in evolution – this would correspond to convergent evolution or horizontal gene transfer).
Joe:
First things first- Linnean taxonomy, ie the observed nested hierarchy with animals, has nothing to do with evolution, guided or unguided. It was created to exemplify a common design. Evolutionists stole it, changed the headings and said theirs can also explain it. Note- NOT predict it, explain it. If anything nested hierarchies are evidence for our cleverness, nothing more.
This is a verbatim copy of a bullshit claim he already made days ago (see above) has already been debunked (which Joe, as always, simply ignored) – is Joe G. just an idiot or is he lying ? You decide.
Btw, evolutionists didn´t steal linnean taxonomy, linnean taxonomy is a tool for classification of living species, it has nothing to do with modelling ancestor-descendant relationships.
All species are on the SAME level. Andy didn’t seem to understand that. But that is because he notion of a nested hierarchy is a non-nested hierarchy with one species giving rise to two (or more).
He´s referring to the Knox paper again which suggests a refinement of taxonomic terminology that has merits, but is neither established nor used in practice (see above). The term “nested hierarchy” is used in Biology (and virtually all other fields exactly as I explained it (or as Douglas Theobald explained it at Talk Origins).
See also:
http://onlinelibrary.wiley.com/doi/10.1046/j.1439-0469.2002.00211.x/abstract
and:
http://www.faculty.biol.ttu.edu/strauss/Phylogenetics/Readings/deQueirozGauthier1992.pdf (seminal review that has been cited over 500 times already, this provides the definitions of taxonomic terms as they are accepted and used in practice.)
All species are on the SAME level.
…
Transitional forms are species too. They are defined as having a mix of defining characteristics from two other species. A mammal-like reptile doesn’t qualify as a mammal (not enough defining characteristics), nor does it qualify as a reptile (not enough defining characteristics). So you would either have to throw it out OR make more “branches” by redefining everything and using fewer and fewer defining characteristics for each set. You would have to do this for each alleged transitional form. And your scheme would become a mess very quickly. And its objectivity would diminish as more “branches” are added.
This is simply unbelievable. This has been explained to him at least a dozen times now.
He seems to believe that all species, alive or extinct, have to go to the lowest level of classification (apparently because he now combines his misconceptions about Linnean taxonomy (where a species, alive or extinct, would always be at the lowest level of classification (this was a time when no one even thought of the idea that entire species could go extinct for fucks sake) and which has nothing to do with modelling common ancestry because no common ancestry between species was assumed) with his misconceptions about phylogenetics (where common ancestry is explicitly modelled).
Extinct species correspond to internal nodes (not the entities at the leaves / tips of the tree) or to extinct lineages in a phylogenetic tree (which shows ancestor-descendant relationships). And in a cladogram, explicit ancestor-descendant relationships are not shown, it shows how monophyletic groups (groups that include an ancestral entity (which could be a single organism, a species, or a group of species (it´s not specified)), all their descendants and nothing else, are related to each other. A cladogram still implies ancestor-descendant relationships (unlike a linnean classification) and descendants branch of from their ancestors.
And even if all ancestral forms were still around, both phylogenetic trees and cladograms would still correspond to nested hierarchies because it would still be true that descendants are more similar to their ancestors than to any randomly selected other taxon and that the relationships to ancestral nodes explains the variation in descendants!
What would change is, that the groups we are used to (e.g. “Mammals”) would no longer be meaningful, because all transitional forms that connect a putative group to it´s most closely related group would still be around – you could simply replace both groups by a new one that combines them, and continue doing that until you are left with just one group – none of these groups would be any more meaningful than the others.
What would not change is, that any two sister taxa at the tips of the hierarchy are more similar to each other and to their ancestor than to other randomly selected taxa (and the same obviously applies to all higher levels in the hierarchy), it would still be a nested hierarchy. This is the inevitable outcome of descent with gradual modification from a common ancestor as I tried to explain to Joe G. *many* times.]
Joe G. just can´t stop showing off how much of an IDiot he is.
He´s still complaining that I misrepresented his words, which is funny, given how I quoted him exactly and always linked to his original posts.
Then he lies about never having claimed to say:
that evolution from a common ancestor does not predict a nested hierarchy of similarities
Joe says:
Nope, I never said, thought nor impled such a thing. IOW Andy thinks I am wrong because he is too stupid to grasp the English language.
Oh really Joe ? Never said or implied ?
I already quoted him above:
An Army is a nested hiearchy [sic]. Just about anything can be placed into a nested hierarchy. However with gradual evolution we would expect to see a smooth blending of deining [sic] traits, and that would ruin a nested hierarchy based on traits.
Source.
He seems to be embarrassed of what he wrote and now tries to lie about it.
He proceeds by demonstrating that he still doesn´t understand how phylogenetics works:
What a moron. All species are on the SAME level. Linnean taxonomy is the nested hierarchy. Phylogenetic trees are non-nested hierarchies. Our bet pertains to nested hierarchies only.
Phylogenetic trees are non-nested hierarchies because they do not display summativity. In a phylogenetic tree we have one giving rise to two or more.
This has now so often explained to him that I´m getting bored. He just doesn´t understand that Linnean classification and phylogenetics are two different things, Linnean classification has nothing to do with common ancestry, phylogenetics does – cladograms and phylogenetic trees do not treat extant species like extinct ones because they DO model common ancestry. This shouldn´t be that hard to understand but we are dealing with an IDiot here.
And he still thinks that the Darwin quote mentioned above supports his Bullshit because he is to stupid to understand this explanation:
What Darwin tried to communicate in this quote was, that demarcation criteria between groups of related organisms have been created by extinction. Think about it, if we assume that all organisms are descendants of a shared common ancestor and modifications happened gradually – how would we classify organisms if every organism that ever lived were still alive today? There would only be one meaningful classification, one group that encompasses all life, because there would be smooth gradual transitions from every form to a closely related form. That´s what we would get with universal common descent + gradualism + ubiquitous immortality. We could still arrange species by similarity within ONE group that encompasses all life, but objective distinctions betweendifferent groups (or any form of hierarchical classification) would be impossible.
As already explained above, if this thought experiment were true, nothing would change about the fact that cladograms and phylogenetic trees would still be nested hierarchies. What would change is, that we could no longer objectively cut off any branch in these trees and treat it like an objective classification (e.g. “Mammals”) – all such putative groups would be equally subjective and you could always simply combine a putative group with it´s most closely related group into one bigger group, and keep doing that until only one group is left (which encompasses all life).
And a further pragmatical problem, if this thought experiment were true, would be, that phylogenetics studies based on morphological traits would be incredibly hard (even impossible in some cases) while phylogenetics studies based on molecular characters would be MUCH easier (even individuals if the same species, which are morphologically indistinguishable, still have detectable differences on the genetic level in virtually all cases).
The funny thing is, that Darwin explains this clearly after Joe´s quote (what ? did you expect that creationists actually read their sources ?
And finally, he tries to argue that Douglas Theobald (yes, the same guy that wrote a long essay on evolution and nested hierarchies) supports his idiotic ideas – you can´t make this shit up.
Joe provides this quote from Theobald:
Most existing species can be organized rather easily in a nested hierarchical classification. This is evident in the use of the Linnaean classification scheme. Based on shared derived characters, closely related organisms can be placed in one group (such as a genus), several genera can be grouped together into one family, several families can be grouped together into an order, etc
And then claims:
LINNEAN CLASSIFICATION is the nested hierarchy you stupid fuck. That means that Theobald agrees with what I said.
And if the IDiot would have kept reading, he might have noticed what Theobald says just three sentences after that:
Most importantly, the standard phylogenetic tree and nearly all less inclusive evolutionary phylogenies have statistically significant, high values of hierarchical structure (Baldauf et al. 2000; Brown et al. 2001; Hillis 1991; Hillis and Huelsenbeck 1992; Klassen et al. 1991).
Theobald was pointing out that the fact that Linnean classification works, means that a hierarchical classification works. And the nested hierarchies that Theobald goes on to discuss are not ones that have nothing to do with ancestor-descendant relationships but rather phylogenetic trees. That´s the entire point of his essay – Joe G. managed to ignore pretty much every context that comes before, or after this quote
And that´s why you should never trust a quote coming from a creationist.]
