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There has been a mammoth conversation going on over on another post,  Creationist stakes $10,000 on contest between Bible and evolution. Regular IDist commenter, JoeG, is a major proponent of pseudoscientific guided evolution. That means to say he broadly agrees to evolution, but claims there is no evidence – it is unguided and there is plenty of evidence that it is guided. This is despite the fact that he neglects to ever provide any of this evidence whilst at the same time demanding that we provide positive evidence that evolution is unguided. I am no evolutionary biologist, which is why I have declared that this is like asking to prove a negative, such as proving that unicorns don’t exist – we perhaps can’t prove a lack of guidance, though we can infer an awful lot and look at probabilistic arguments.

Anyway, the great part of this story is that my co-writer here at ATP is Andy Schueler. For those of you who don’t know him, he is a molecular evolutionary biologist. I love watching him in arguments about evolution because he really does know his stuff. He is awesome.

So, on this other thread, there is a big set of nebulous arguments going on – well worth looking over to see how the mind of an IDist works. They make lots of demands, give huge amounts of assertions, make wild claims. But they never answer questions directed at them, never substantiate claims.

So, one such exchange was about nested hierarchies. These, for those who don’t know, are defined as:

Taxonomy is based on the fact that all organisms are related to each other in nested hierarchies based on shared characteristics. Most existing species can be organized rather easily in a nested hierarchical classification. This is evident from 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.[39] The existence of these nested hierarchies was recognized by many biologists before Darwin, but he showed that his theory of evolution with its branching pattern of common descent could explain them.[39][40] Darwin described how common descent could provide a logical basis for classification:[41]

All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical; that community of descent is the hidden bond which naturalists have been unconsciously seeking, …
Charles DarwinOn the Origin of Species, page 577

So there is this discussion about nested hierarchies on the thread. JoeG, given the subject matter of the OP, muttered these immortal words:

An Army is a nested hiearchy. Just about anything can be placed into a nested hierarchy. However with gradual evolution we would expect to see a smooth blending of deining traits, and that would ruin a nested hierarchy based on traits.

Linneaus, a Creationist, made his nested hierarchy based on a common design.

And I will put up $10,000 US to prove that I understand nested hierarchies better than you.

BTW, chump, we do NOT see a strict nested hierarchy with prokaryotes. Ya see HGT ruins it. You lose, again.

Before I talk about the content per se, let me say a little thing about etiquette. Firstly, at my blog, I invite people here of all different worldviews to discuss things with humility and with composure and without unnecessary rudeness. Andy is a molecular biologist who works with these ideas every day. Calling him a chump is seriously miscalculated and unnecessary.

Andy’s retort:

An Army is a nested hiearchy. Just about anything can be placed into a nested hierarchy.

No. In fact, most things that are designed can not be placed objectively in a nested hierarchy (hint: whether the distribution of features is hierarchical or not can be precisely quantified and statistically tested) . Take cars or watches, or computers for example (because technological novelties (e.g. Airbags or Navigation systems for cars) could be included in ALL models, and their inclusion usually reflects the price of the product, not how close it is related to another product (no matter how you measure “relation” – common manufacturer, common inspirations etc. – all lead to the same result)).

Such a free mixing of features that is not constrained by a relationship like common descent would lead to trees that are not significantly hierarchical or even anti-hierarchical.

Just try it for yourself, define a similarity matrix for cars (or computers, or cell phones) in the same way Biologists define one based on morphology (or development or what have you), then infer a UPGMA or NJ (you could also use ML or bayesian statistics, but you would have to customize the statistical model yourself for such a non-standard application) phylogenetic tree for this matrix (virtually all software for this is freely available, use phylip for example) – and calculate the consistency index (or any comparable measurement for which a test statistic is available). Then compare this to the consistency index for the trees of ten randomly chosen gene families and for the trees for plants and animals inferred from morphology.

You´ll see the difference – one kind of trees is significantly hierarchical (the ones for biological entities), while the other is not (the trees for virtually all designed entities).

Linneaus, a Creationist, made his nested hierarchy based on a common design.

True, as I said, common design is trivially compatible with a strict nested hierarchy, but it would also be trivially compatible with an anti-hierarchical distribution of features and anything in between. Since “Design” has no constraints whatsoever (can you explain precisely what the “Designers” could NOT do ?), “Design” is trivially compatible with any observation, but also refuted by none and supported by none. Common descent on the other hand makes specific predictions and thus can lead to hypotheses that refute or support the claim (three of which are mentioned above).

And I will put up $10,000 US to prove that I understand nested hierarchies better than you.

CHALLENGE ACCEPTED.

Now let me prove that up until at least two months ago, you did not have the foggiest clue about what a nested hierarchy is. You (commenting as user “frisbee_kid” (do you deny that this was you ?)), posted the following comment:

As for nested hierarchies- LoL!. The fact that the theory of evolution posits a gradual change, which means there would be many, many transitional forms, it is clar that the theory does not expect a nested hierarchy based on traits. Transitional forms by definition means there would be organisms with a ixture of defining traits, which would ruin a nested hierarchy based on traits.Link

=> Ergo, you were completely and utterly clueless about what nested hierarchies are just two months ago, and anything you might know about it has been learned within this timeframe. I on the other hand studied Molecular Biology and Bioinformatics and study phylogenetic trees (which requires an understanding of nested hierarchies) regularly at work since roughly five years (if I count the time since I started working mostly independently) and my work has been published in peer-reviewed journals.

Evidence for those claims can of course be provided and I´ll happily provide you with copies of my academic certificates and publications (and my bank account of course).

Now I hope you honor your commitment and thanks a lot for ten thousand bucks! 🙂

And I have taken basic biology courses. I ghave taken advanced courses too. So have the thousands of biologists who say that unguided evolution is bogus and untestable.

Riiiiight. Thousands of Biologists! And here I am working as a Biologist and have never met a single one of those alleged “thousands of Biologists”, not at work, not at a conference and even if you count my online activities I have encountered just ONE Biologist (who studied Biology but does not work as a Biologist) who happens to doubt Evolution (which is by definition unguided).

Hell, not even for that ridiculous “Dissent from Darwin list”, which includes quite a lot of engineers but VERY few Biologists, could you find those “thousands of Biologists”, which leads me to believe that you simply made this shit up.

Btw, I don´t know many Biologists who would NOT agree with this statement:

“We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

=> Because few Biologists are so ignorant about evolution as to reduce it to “random mutation and natural selection” (which wouldn´t explain the Peacock´s tail or Stickleback armor or Intronization events – to mention just three examples out of thousands of possibilities).

Positive evidence for entities has been presented.

Your “positive evidence” amounts to “I don´t understand it, which means no one else understands it, which means it cannot be understood in principle, which means it must be magic.”

Hint: an argument from ignorance is actually the precise opposite of “positive evidence”.

OTOH you don’t have any evidence for unguided evolution. All you have are bald declarations.Now you are just lying, you can´t be that stupid. I´ve walked you through three specific examples in a way that even a complete idiot should be able to understand. And your replies so far amount to hilarious misunderstandings of Lenski´s work and nested hierarchies and to this lie right here.

And IDists understand ID better than SETI researchers.What is there to understand ? To be a Cdesign Proponentsist, you could simply take a creationist “textbook” and replace all instances of “God” by “Designer” and “Creationists” by “Design proponents” (or Cdesign proponentsists if you are too stupid for the job). Alternatively, you simply make up new shit as you go along – take CSI for example, it´s simply hilarious to watch you guys come up with countless totally different (but all equally useless and inconsistent) definitions. How about we compare CSI sensu Dembski (all different versions of course), sensu VJ Torley, sensu KairosFocus and sensu seven other randomly selected Cdesign proponentsists, that should be fun, shouldn´t it ? ;-).

If you ask ten different Evolutionary Biologists about the mean and variance of fixation times for neutral mutations in an asexual population of a given size (for example), they will all give you the exact same answer (and could even provide you with a mathematical proof and experimental evidence). And that is the difference between scientists and Cdesign proponentsists.

So there it is. A challenge that he, JoeG, a kind of biological nobody, knows more than a molecular evolutionary biologist about nested hierarchies. This, after a previous conversation in which JoeG had shown merely two months before that he didn’t have a clue what they were!

But JoeG seems unfazed by his own utter arrogance and continues:

No, Andy- it all depends on what criteria is used- just ask the nested hierarchy experts- I have.

And I am correct- transitional forms, by their very nature, contain a MIX of defining characteristics. THAT violates a nested hierarchy. Obvioulsy 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.

For example if your sets require that ten characteristics be present and you have a transitional that only has 5, where do you put it? You have to redefine your parameters. IOW if all of the alleged transitionals were still alive we wouldn’t see a strict, objective nested hierarchy.

Design is NOT compatible with any observation. You are just ignorant.

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”.

And please demonstrate that evolution prevents traits from being mixed and matched. What is the law that prevents such a thing.

Ya see evolutionism is OK with any pattern- that is obvious by the total lack of nested hierarchy wrt prokaryotes.

And you didn’t walk anyone through anything wrt unguided evolution.

Oh and no evo can demonstrate the fixation of any allele.

What’s interesting here is that this Denton chap wrote this book in 1985. Not a recent blockbuster. The book could not pass peer review because it was so erroneous and Denton has since changed his views on evolution! Wow. Good use of resources there! Philip Spieth, Professor of Genetics at University of California, Berkeley, reviewed the book saying “evolutionary theory is misrepresented and distorted; spurious arguments are advanced as disproof of topics to which the arguments are, at best, tangentially relevant; evolutionary biologists are quoted out of context; large portions of relevant scientific literature are ignored; dubious or inaccurate statements appear as bald assertations accompanied, more often than not, with scorn.” Denton did not even understand criticisms about his use of his idea of molecular equidistance!

Anywho, there you go. Andy continued:

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).

You owe me ten thousand bucks Dude.

and:

No, Andy- it all depends on what criteria is used- just ask the nested hierarchy experts- I have.

There is only one criterion – does the data show significant hierarchical structure or not. Which means you need a measurement for “hierarchical” and an associated test statistic. Established measures would be the consistency index for example (key publication here). Now, my claim is, that biological entities can be objectively assigned to nested hierarchies (i.e. associated with statistically highly significant measures of hierarchical structure), while most designed objects (watches, cell phones, computers etc.) can not. This has been established for decades in the scientific literature (see publication above + more recent papers that cite it or any textbook on phylogeny inference and references therein (and many of the college level textbooks on Evolutionary Biology)).

You referring to an anonymous alleged expert on nested hierarchies who contradicts all published literature on the subject is not exactly convincing.

And I am correct- transitional forms, by their very nature, contain a MIX of defining characteristics. THAT violates a nested hierarchy.

:-D. Dude, this is about the single dumbest thing that you could have said about this subject, seriously – I really could not imagine a more outrageously stupid comment about nested hierarchies. Let me walk you through that reeeaaal slow. You seem to think that mixing features violates a nested hierarchy. If this would be true (hint: it isn´t), then the very existence of nested hierarchies would be a logical impossibility, because the only collections of entities where there is ZERO mixing of features, are collections where all entities are either exactly identical or completely different.

But you are not interested in relationships between entities that are identical (it wouldn´t even make sense – imagine a “hierarchy” of 1000 instances of the number 1), you are interested in hierarchies of distinct entities! But since you just ruled out ANY mixing of attributes – you can only classify entities that have NOTHING in common and that all have the SAME distance / similarity to each other (which is INFINITY (or the maximum possible distance otherwise) and ZERO respectively). And a nested hierarchy for entities that have all the EXACT SAME similarity / distance to each other is a logical impossibility. Congratulations! You have just proven, using IDiot logic, that nested hierarchies cannot possibly exist.

Using actual logic, it looks slightly different, here, entities in a hierarchy can (and always do) mix attributes. And the criterion for a significant hierarchical structure is that the entities do not mix attributes ARBITRARILY, but rather in a hierarchical way (who would have guessed ?!). 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, 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.

Will you honor your commitment now and hand over the 10000 bucks or do you chicken out ?

Obvioulsy you don’t know anything about nested hierarchies and you think that your ignorance refutes me.

Yes, we´ve seen above how much we both now respectively about nested hierarchies…

Hint: a big mouth is dangerous when you don´t have the foggiest idea what you are talking about ;-).

If you have a mix of traits then a nested hierarchy is violated. period. End of story.

No, as I demonstrated above, using your “understanding” of nested hierarchies, the very existence of nested hierarchies is a logical impossibility.

Boy do you look like a fool now…

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”.

Actually, they do. LGT notwithstanding (although LGT obviously does reduce the level of hierarchical structure). But I´d prefer to enter this discussion once you´ve demonstrated that you finally begin to understand what a nested hierarchy even is (another hint: it´s not a binary attribute).

Design is NOT compatible with any observation. You are just ignorant.

Oh really, yet neither you, nor any other IDiot, can explain what the alleged “Designers” could NOT do and which constraints are thus put on possible observations if the “Design hypothesis” is true, no matter how often you are asked (as I did above). Which means you are either lying, or stupid. Which one is it ?

And please demonstrate that evolution prevents traits from being mixed and matched. What is the law that prevents such a thing.

Actually traits are being mixed, your idiotic misconceptions that ANY mixing of characters violates a nested hierarchy has been addressed above.

As to your question why evolution from a common ancestor predicts a nested hierarchy of features, I guess we have to start at the very basics (Dude, it get´s less and less believable that you had any Biology classes or any form of higher education for that matter…).

You might have noticed that children tend to be different from their parents, but still much more similar to them than to randomly chosen other people (and MUCH more similar to them than to a randomly chosen non-human animal). That is because genetic material is actually inherited from your parents (were you homeschooled ?). And, believe it or not, this form of vertical transfer of genetic material is actually by far the most common form of transfer and for many species even the only one. What this means is that the offspring produced in any species will, statistically, always be more similar to their parents than to other individuals individuals that are not their parents and much more similar to their parents than to members of other species. If you extrapolate this process into the future and combine it with the variation (this is caused by so called “Mutation”, but we´ll get to that another time), you get a nested hierarchy of similarities between organisms. Since vertical transmission is dominant over lateral transmission of genetic material, and sometimes even the only mode of transmission, descent with modification from a common ancestor necessarily produces nested hierarchies of similarities (for a mathematical treatment, see Harris, T. E. (1989) The Theory of Branching Processes. New York: Dover.).

Caveat: the distribution of very fast evolving characters between distantly related taxa will be indistinguishable from random noise (that´s why fast evolving characters are preferred for studying very closely related species while slow evolving ones are preferred for distantly related ones).

Ya see evolutionism is OK with any pattern

Ok, you don´t seem to be lying, you seem to be a genuine idiot.

that is obvious by the total lack of nested hierarchy wrt prokaryotes.

Actually, prokaryotes show (unsurprisingly since vertical transmission is more frequent than lateral) a highly significant degree of hierarchical structure, which is (again unsurprisingly) lower than the degree of hierarchical structure for species where LGT virtually never happens.

And you didn’t walk anyone through anything wrt unguided evolution.

Don´t blame me for your mental deficiency.

Oh and no evo can demonstrate the fixation of any allele.

Complete and utter moron, or troll, or both…. After reading this, I´d say it could be any of the three.

And so it continues. Some could say that this is an evolutionary smackdown. Yes, Andy is being harsh on JoeG verbally, but if you have seen the history of Joe’s comments, this is totally understandable. The guy came here months ago and arrogantly started demanding, accusing, shouting and certainly not being dialectically discursive!

What do we do? Does Andy send a bill to Joe? Is Joe now indebted to Andy? How do we sort this wrangle? Do we call the lawyers?

[UPDATE: http://intelligentreasoning.blogspot.co.uk/ – this is JoeG’s website. This is his tagline:

“Promoting, advancing and defending Intelligent Design via data, logic and Intelligent Reasoning and exposing the theory of evolution as the nonsense it is. I also educate evotards about ID and the theory of evolution one tard at a time and sometimes in groups”

Which is a flat contradiction. It is a tirade of invective. The only comments on his posts appear to come from himself. Hey-ho, judge for yourself. As I have said, I welcome his voice here, as long as it is reasonable and genuinely open.]

Jonathan MS Pearce

A TIPPLING PHILOSOPHER Jonathan MS Pearce is a philosopher, author, columnist, and public speaker with an interest in writing about almost anything, from skepticism to science, politics, and morality,...