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JoeG´s shenanigans continue

I´m skeptical that anyone is still interested in seeing more of Joe G´s shenanigans (if you missed the story, it´s the Cdesign proponentsist that challenged me to a $10,000 bet, lost, and then chickened out ). If you are bored of this guy, leave now ;-).

But since he seems to be kind of obsessive after losing our $10,000 bet and can´t stop blogging about it, I´ll give a brief response to his latest claims – although virtually everything has already been addressed many times in the comments on the earlier threads, but JoeG. has a habit of ignoring counterarguments and simply repeating his bullshit over and over again.

JoeG´s claims are evolving constantly since he apparently can´t make up his mind about what he actually wants to claim.

To give an example, his very first claim related to nested hierarchies on this blog was transitional forms violate a nested hierarchy, but now, he´s not too happy with that anymore and decided that it should rather be I said that if all the alleged transitional forms still existed that we could NOT form a nice strict, oderly nested hierarchy (without retracting his earlier claim of course, what else would you expect from a Cdesign proponentsist).

So now we are no longer talking about the real world, but rather about a thought experiment where all extinct transitional forms are still around. He tries to justify this by claiming that extinction is not predicted by evolution, but more on that later.

Another issue with Joe G´s arguments is his abysmal reading comprehension. A degree of reading comprehension that hilariously led him to conclude that a Talk Origins essay by Douglas Theobald (highly recommended!), which has the sole purpose of demonstrating how evolution predicts nested hierarchies of species and how this prediction was confirmed, agrees with him. He quoted this part of Theobald´s essay many times (e.g. here):

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.

….

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 genuinely believes that this supports his earlier argument (”that if all the alleged transitional forms still existed that we could NOT form a nice strict, oderly nested hierarchy” – see above). It was pointed out to him many times that Theobald does not agree with him and he simply didn´t understand what he was reading, example:

No, he doesn´t [agree with you] 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 [criteria for objective nested hierarchies] 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 [measuring the degree of hierarchical structure] would be 1 [maximal]). What reduces the degree of hierarchical structure is the independent (i.e. not explainable by relation to parent node) emergence of features.”

He received this reply and similar replies many times, and either didn´t acknowledge or address them at all, or argued that ancestral species “are still species” and thus have to go to the lowest level in the hierarchy together with extant species (which is complete nonsense in a phylogenetic tree – descendants obviously branch off from their ancestors). At first it was a complete mystery to me why he just doesn´t get it since this really is not that hard to understand, but after one of his recent posts, it finally makes sense. He stumbled upon this part of Theobald´s essay:

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

He noticed the phrase “Linnaean classification”, which hilariously led him to conclude that the essay is about Linnaean classification (where species, alive or extinct, are indeed all at the lowest level of classification), and thus concluded that the essay supports his argument.

Let me briefly point out the difference between Linnaean classification and phylogenetics. Both subjects deal with nested hierarchies, one being a system to assign organisms, based on their attributes, to groups which are contained in more general groups (Linnaean classification), the other being the study of evolutionary relationships between organisms.

Joe G´s arguments regarding on what evolution allegedly does or does not predict wrt nested hierarchies is based on Linnaean classification and only Linnaean classification. But he only now bothered to make that clear (“making it clear” in this case means “LINNEAN CLASSIFICATION is the nested hierarchy you stupid fuck. That means that Theobald agrees with what I said.”)

And this is what I mean when I talk about his abysmal reading comprehension. A person with a little reading comprehension might have noticed:

– that Theobald uses the sentence “More precisely, if the phylogenetic tree of all life gave statistically significant low values of…” in the sentence that Joe G. thinks supports his argument.

– that Theobald prefaces his essay with an introduction to phylogenetics, not Linnaean classification.

– that the results which Theobald presents and discusses relate to phylogenetic trees, not Linnaean classification.

– that my intial argument regarding nested hierarchies, my replies to him (and the replies from several other commenters) referred with almost no exceptions to phylogenetic trees, not Linnaean classification (and unlike Joe G. we bothered to make clear what we were talking about right from the beginning).

His “clarification” (“LINNEAN CLASSIFICATION is the nested hierarchy you stupid fuck. That means that Theobald agrees with what I said.”, see above) would have been very helpful 10 days ago when this all started and would have saved us a lot of time). So, to make that clear, Joe G. rests his entire case wrt what evolution does or does not predict on Linnaean classification, not phylogenetics

Joe G. must have kind of understood though, that all his nonsense about transitional forms allegedly “ruining” a nested hierarchy was completely irrelevant in the context of phylogenetics (which still never motivated him to clearly state that his claims in this context are limited to Linnaean classification and ONLY Linnaean classification until now, see above), because he desperately tried to argue that phylogenetic trees are not “nested hierarchies” already before his “clarification”.

His evidence for this claim, that phylogenetic trees are not nested hierarchies, is a 1998 paper by Eric Knox and this link.

The Knox paper proposes a refinement of taxonomic terminology, which distinguishes between “non-nested”, “semi-nested” and “fully-nested” hierarchies. His criteria to distinguish between those three types of hierarchies is based on whether the sum of the elements at a lower level of the hierarchy are equal to their parent node at the next higher level of classification.

An example would be the Linnaean classification scheme, the Genus (second lowest level in the hierarchy) “Homo” contains all species (lowest level of the hierarchy) that belong to this Genus – the whole (Genus) is thus the exact sum of it´s parts (Species corresponding to this Genus), and Knox refers to it as “fully-nested”.

For phylogenetic trees (which show ancestor-descendant relationships), Knox argues that lower levels in the hierarchy are not fully contained within their parent nodes due to the creative power of evolution – the “sum” of the descendants that branch of from an ancestor are not equal to their ancestor, they are more than their ancestor (while in a Linnaean classification, for example, the sum of all species that are part of the Genus Homo is indeed equal to the Genus Homo). The Knox paper furthermore implies that cladograms (which look very similar to phylogenetic trees but are interpreted differently, more details in a later post) are “semi-hierarchical”.

However, as was pointed out to Joe G. at least half a dozen times (and never acknowledged or addressed by him), this refined terminology is neither established in Biology, nor used in practice (both of his sources are inspired by systems theory). What is established and used in practice (not only in Biology but also in the social sciences for example), are definitions like the one Ernst Mayr gave:

The arrangement of entities in a hierarchical series of nested classes, in which similar or related classes at one hierarchical level are combined comprehensively into more inclusive classes at the next higher level.

Source.

Or the definition for nested hierarchies as also used in the social sciences:

Inclusion hierarchy [synonym of nested hierarchy, AS]: Sometimes, hierarchy is used to refer to a recursive organization of entities. For example, in the essays discussed in section 2 below, Herbert Simon defines hierarchy with his famous “Chinese boxes” image: “In application to the architecture of complex systems, ‘hierarchy’ simply means a set of Chinese boxes of a particular kind. A set of Chinese boxes usually consists of a box enclosing a second

box, which, in turn, encloses a third – the recursion continuing as long as the patience of the craftsman holds out. The Chinese boxes called ‘hierarchies’ are a variant of that pattern. Opening any given box in a hierarchy discloses not just one new box within, but a whole small set of boxes; and opening any one of these component boxes discloses a new set in turn.”

Pumain, Denise (2006). Hierarchy in Natural and Social Sciences. New York, New York: Springer-Verlag. (page 85)

The criterion for nested / inclusion hierarchies, as widely established, is a principle of containment of lower level elements within higher level elements of the hierarchy, not equality between them. In fact, the most commonly given example of a nested hierarchy, the the matryoshka dolls, would not be an example of a nested hierarchy anymore if we used the principle of equality instead of containment (the bigger matryoshka dolls contain other matryoshka dolls but are not equal to them / composed of them).

However, what is even more important, even IF we would accept the terminology suggested by Knox (and proposed by Joe G.), all that would mean for our disagreement is, that the phylogenetic trees and cladograms generated by evolutionary biologists are “non-nested” and “semi-nested” respectively, but contain within them ALL the information of a fully-nested hierarchy!

If we remove information from a phylogenetic tree (specifically, the explicit representation of time or similarity (both can be used in a phylogenetic tree) and the information about ancestor-descendant relationships), but keep the ordering intact, we get a “fully-nested” hierarchy sensu Knox (for more details, see the Knox paper, but I´ll also explain this in more detail in a follow-up post (one that focusses on science, not creationist-misconceptions, I promise 😉 )).

So, even if we would accept Joe G´s argument here (which we don´t have to for the reasons explained above), evolution would still produce nested hierarchies and Joe G would still be wrong.

One of the other claims that Joe G. repeated ad nauseam was, that evolution with gradual modification from a common ancestor does not predict a nested hierarchy. But why he thinks that is depends on his mood and changes constantly.

On one day, it might be because he thinks that evolution predicts transitional forms, meaning that it cannot predict nested hierarchies (e.g. here). On another day, it might be because he thinks that evolution might lead to a nested hierarchy, but only if extinctions happen, which, according to Joe G., evolution doesn´t predict, ergo it doesn´t predict nested hierarchies ( e.g. here). Sometimes, it is also because he currently thinks “Ya see evolutionism is OK with any pattern”, or because he currently thinks that evolution could not produce a nested hierarchy of species because it can´t control which traits are gained and lost “Ya see with evolution traits can be lost if that is what survives. Or traits can stay the same, meaning you will only have one set. So evolutionism can live with a nested hierarchy and it can definitely live without one.”

Two of those reasons (the last two) are so stupid that it really requires little more than understanding where babies come from to see why they are wrong, as I tried to explain to him multiple times, including at the very beginning of our disagreement (addressing the hilariously stupid question “please demonstrate that evolution prevents traits from being mixed and matched. What is the law that prevents such a thing?”).

He could also easily have known why the other two reasons are wrong if he had actually read what Darwin wrote about this topic with a little reading comprehension, and would have considered the context instead of relying on just a short mined quote.

Darwin did predict a nested hierarchy of species:

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.

Note that the ordering that Darwin refers to is a phylogeny (NOT something equivalent to a Linnaean classification, as Joe G. seems to be unable to understand).

Darwin also extensively discussed extinction and the reasons leading to it in “On the Origin of Species” in multiple chapters (including the one where Joe G´s quote was mined from), it also contains a chapter that is almost exclusively focussed on extinction, he was also aware that extinction is an empirical fact, and even if he would not have been, it is predicted by his principle of divergence as already expressed before the publication of the Origin in the Darwin-Wallace paper (see point 6, discussed in much more detail in the Origin). And again Joe G. literally could not be more wrong.

Joe G. is also obsessed with a particular quote from the Origin of Species, of which he thinks that it agrees with him. It is this one from chapter 14:

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.

(Darwin still talks about this diagram btw)

Joe G. cites this quote in support of this proposition: “I said that if all the alleged transitional forms still existed that we could NOT form a nice strict, oderly nested hierarchy.” (Source.)

And again we are dealing with Joe G´s complete lack of reading comprehension, a person with reading comprehension might have noticed the last sentence and kept reading further. This is how Darwin continues:

We shall see this by turning to the diagram [again, same diagram as above – AS]: the letters, A to L, may represent eleven Silurian genera, some of which have produced large groups of modified descendants, with every link in each branch and sub-branch still alive; and the links not greater than those between existing varieties. In this case it would be quite impossible to give definitions by which the several members of the several groups could be distinguished from their more immediate parents and descendants. Yet the arrangement in the diagram would still hold good and would be natural; for, on the principle of inheritance, all the forms descended, for instance from A, would have something in common.

Darwin explains how, in a thought experiment where all extinct forms were still around, classification (as in Linnaean classification) could no longer be done objectively. However, a phylogenetic tree (his diagram is one), would “still hold good and would be natural”.

And Darwin is completely right about both claims. All extinct forms being revived would change nothing about the ancestor-descendant relationships in his diagram and it would still be a nested hierarchy (or a non-nested one containing a fully-nested hierarchy if we accept the terminology of Knox – see above).

In this thought experiment, the results produced by phylogenetics studies, would still be objective nested hierarchies. What would change is, that a job as done by Linnaeus (Linnaean classification) could no longer be done objectively. With all extinct forms still being around, no group (e.g. “mammals”) could be defined objectively, because all intermediate forms connecting it to it´s most closely related group would still be around and we could simply replace both groups by one that encompasses both (and keep doing that until we are left with just one group that contains all life). We could classify organisms pragmatically by picking it out forms that are representative for a large group of related forms and classify those, but defining objective groups that are clearly demarcated from their closest relatives would be impossible.

The nested hierarchy corresponding to ancestor-descendant relationships however would still be natural / still be objective (what would change in practice though, is that phylogenetics studies based on morphological characters would be more challenging while phylogenetics studies based on molecular characters would be MUCH easier – but we generally would have a lot more work to do simply because biodiversity on this planet would be much more vast than it is now in this thought experiment).

According to Joe G. I´m also a “lying sack of shit” because I misrepresented his words. Which is funny, because I always link to his exact quotes. The example he gives is this one:

Andy: “our disagreement started with Joe G´s claims that “everything could be placed into nested hierarchies”

Joe: Liar, I did NOT say that. I said just about anything can be placed into a nested hierarchy.

Mea culpa! “Just about anything” is of course not the same as “everything”. I did quote his exact words in the very next sentence and linked to his comment (see right the beginning of this post) and my refutation of his claim is completely independent of whether he said “just about anything” or “everything” (both claims are bullshit, for the same reasons), but of course, misrepresenting “just about anything” as “everything” is still unforgivable.

And while we are talking about lying sacks of shit, how about pointing out that Joe G now claims that he said “Just about anything can be placed into a nested hierarchy” but that does NOT mean it is going to be a neat and orderly nested hierarchy but only after I explained to him why his earlier claim, which did not include the part I highlighted, is bullshit (without acknowledging that he changed his claim of course, as always).

And finally. I´d like to point out again just how easy I made this bet for Joe. I allowed him to pick judges to settle our bet, I even allowed him to pick Cdesign proponentsist judges for our bet, all I cared about was that they are qualified and willing to go on the record. What I said exactly was:

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).

Source.

This is what Joe G. made out of it:

Oops. Andy sez I can use any judges I want. Well Andy I will take Darwin and Denton.

You lose.

Source.

Normally, I would say this makes him a liar and a coward. But now, since it has become so abundantly clear that his reading comprehension is not just abysmal, but rather virtually non-existent, I´m not so sure anymore. As Hanlon´s razor states, “never attribute to malice that which is adequately explained by stupidity”.

But in any case, Joe G. seems to have a clear anger management problem (and I really don´t understand why he is so angry, given that we have generated some traffic for his blog which otherwise attracts 8-10 clicks per day statistically, according to http://www.worthofweb.com – with the ad money he could generate with that, it would only take him roughly 500 years to pay off the money he owes me).

Addendum:

I thought Joe G. would be irrational in his responses to me, but I really underestimated him… Joe Felsenstein (NAS member and one of the authorities in the fields of phylogenetics and population genetics) was another one of Joe G´s recent targets in his blog. Behold this black hole of inanity and viciousness:

Fatman Joe Felsenstein has a new article Does CSI Enable Us to Detect Design?

http://pandasthumb.org/archives/2013/04/does-csi-enable.html

Yes, it does Joe. However you, being a moron, don’t know how to detect anything.

Joe sez:

When Shallit and Elsberry found a hole in Dembski’s theorem, and when I pointed out that the theorem was unable to refute the effectiveness of natural selection (because its specification changed in midstream) we were right.

Earth to Fat Joe Felsenstein- There isn’t any evidence that natural selection can do anything, let alone create CSI. As a matter of fact natural selection requires the existence of CSI.

EVIDENCE- yours is a position that is absent of evidence. So until you actually have some, perhaps you should just keep stuffing donuts into your hole.

Joe spews:

But whether I am right about that or not, Dembski and Marks have not provided any new argument that shows that a Designer intervenes after the population starts to evolve.

No intervention required dickhead. Did Dawkins “weasel” require intervention to reach the target? Do computer prograns require intervention to do what they are designed to do?

OK so Felsenstein still doesn’t have any evidence to support his trope.

Joe Felsenstein, scientifically illiterate joke

Wow… One could of course point out that “you are fat” is not exactly a refutation of carefully laid out arguments, but let´s take the Cdesign proponentsist serious here for a moment. And let´s pass over the hilariously moronic claims that “natural selection can´t do anything” (even for YEC standards, this would be an outrageously stupid claim, YECs usually try to argue that natural selection can only preserve but is useless for generating any kind of novelty, or try to argue how natural selection helped to increase biodiversity after Noah´s flood (based on pre-existing “information” of course) – which is still stupid, but not nearly as stupid as Joe G´s claim here) and Felsenstein´s position being “absent of evidence” (let´s attribute this idiocy to Joe G´s complete and utter lack of reading comprehension again) .

The articles that are being referred to are:

http://www.antievolution.org/people/wre/papers/eandsdembski.pdf (Elsberry & Shallit 2003)

http://ncse.com/rncse/27/3-4/has-natural-selection-been-refuted-arguments-william-dembski (Felsenstein 2007)

http://pandasthumb.org/archives/2013/04/does-csi-enable.html (Felsenstein 2013)

See for yourself and judge if “well, you´re fat” is indeed an adequate refutation of those articles.

And I didn´t cherry pick this post, this is not a particular shocking example from his blog, only a recent one. Several commenters in the earlier threads provided links to posts from him that make this one look well reasoned and polite. Remember, those are the people that oppose evolution.

I happily admit that Joe G. might be a particularly shocking example of the inanity and viciousness we see on the antievolution front, but it´s not as if the more prominent Cdesign proponentsists are much better.

Remember the Judge Jones (the Judge that ruled that ID is not science in the Kitzmiller v Dover case) school of law created by Cdesign proponentsists with a blessing from Dembski ? (which originally had farting noises (yes, I´m not kidding) being played while the Judge Jones caricature was talking – Dembski´s motivation for removing the fart noises is documented here (hint: it has nothing to do with having even a shred of shame, decency or integrity)).