email - August 2016
by Do-While Jones

Arbitrary Classification

Is taxonomy arbitrary or not?

We received this very long email from a professor at a major university in Mexico. He gave his full name and affiliation in his email, but we changed his name to “Pedro” to protect his identity. We aren’t trying to embarrass him or attack him personally—we are discussing the ideas he clearly presents.

Primarily, we want to address his claim that taxonomy (that is, the biological classification system) is not arbitrary. Here’s what he wrote.

Dear Mr. Jones,

I hope you are having a great day. I'm Pedro, teacher of Systematics at the science school of Mexico's best university. It is by this means that I would like to start a friendly discussion regarding the opinions expressed in the science against evolution website. I hope we both get enriched by this discussion. I would like to start this exchange of ideas with counter-arguments against the arguments presented in the "Dinosaur Delusions" article. 1

-First, there are some comments on classification saying it is arbitrary. I think you are lacking some historical context and showing ignorance with respect to the current ways of classifying life. At the time of Bakker's publications the prevailing school of systematics was the Darwinian "evolutionary systematics". Nowadays cladistics is regarded as superior to evolutionary systematics. The latter one indeed arbitrarily divided groups of animals based on their adaptations. Cladistics avoid this limitation by providing a repeatable and unbiased way of classifying organisms: a group needs to include an ancestor and all of its descendants (this is called a monophyletic group). Therefore, it would be arbitrary to exclude a certain group of descendants from that group. That's why birds are dinosaurs. All dinosaurs (e.g. Triceratops and Tyrannosaurus) share a common ancestor, and so the group Dinosauria needs to include all descendants of that ancestor, one of which is birds. Also, please remember that not all dinosaurs are birds, but all birds are dinosaurs (it's not that hard to picture: not all Americans are Ohians, but all Ohians are American). The same applies to the clade Reptilia. Since dinosaurs are descendants of the most recent common ancestor of all reptiles, they are reptiles. Therefore, all dinosaurs are reptiles but not all reptiles are dinosaurs, and, since birds are dinosaurs, all birds are reptiles but not all reptiles are birds. Note that groups are not formed based in similarity, but in relatedness. If my dad was blue-eyed and I was brown-eyed we would still be family.

-The issue of "cold" or "warm-blooded" dinosaurs is not a matter of opinion. Evidence now suggests non-avian dinosaurs had a unique metabolism (similar to what you guys jokingly state as "tepid-blooded"). As you pointed out, there was evidence suggesting they were cold blooded and evidence suggesting they were warm blooded, but those two pieces of evidence are not contradictory when you consider them to have a unique metabolism, an idea supported by several lines of evidence.

-Sometimes there are evolutionary patterns, sometimes there aren't. Evolution is an [sic] stochastic phenomenon (as computer scientist I think you know what that is). Evolution is dynamic and it's [sic] mode and tempo is [sic] dependent on several factors. If there is not a trend towards miniaturization in Theropoda it doesn't mean that a particular population of theropods couldn't undergo miniaturization, even if other populations didn't.

-All science evolves. We now know Newtonian mechanics are not followed in too big and too small scales. As our capacity to gather more and more reliable evidence improves (mainly thanks to technology) some theories need to be re-thinked. Newtonian mechanics are still valid, as is evolutionary theory, but both theories have become more refined and have now more intellectual branchings. There is not a single line of evidence denying evolution, we just now know it is more complex than expected. In fact, the changing nature of theories is their strength compared to religion, which is dogmatic and tyrannical. Theories change as more evidence is gathered, regardless of whether we like it or not, while religion generally doesn't change and if it does it's according to the interests of a few and not because of evidence.

-Finally, Ryan's crazy theories can in fact be proven wrong, contrary to his statements. We know convergence exists because rigorous methods of reconstructing life trees support its existence. Trees and evolutionary hypotheses are not built arbitrarily, but are built based on rigorous mathematical and statistical methods that take several lines of evidence into account. The recognition of homology and convergence is based on these rigorous methods.

I hope this is the beginning of a friendly and enriching exchange of ideas on several topics.



What is “Arbitrary”?

Some people are unclear on the concept of “arbitrary”. So, let’s start with the definition of arbitrary, and then explore the concept. According to Merriam-Webster,

Full Definition of arbitrary
1 :  depending on individual discretion (as of a judge) and not fixed by law (the manner of punishment is arbitrary)
2a :  not restrained or limited in the exercise of power :  ruling by absolute authority (an arbitrary government)
2b :  marked by or resulting from the unrestrained and often tyrannical exercise of power (protection from arbitrary arrest and detention)
3a :  based on or determined by individual preference or convenience rather than by necessity or the intrinsic nature of something (an arbitrary standard) (take any arbitrary positive number) (arbitrary division of historical studies into watertight compartments — A. J. Toynbee)
3b :  existing or coming about seemingly at random or by chance or as a capricious and unreasonable act of will (when a task is not seen in a meaningful context it is experienced as being arbitrary — Nehemiah Jordan)

To some people, “arbitrary” is a pejorative word, primarily because of the tyrannical aspects of definition 2b. We imagine Dr. Sigmund Freud explaining it this way: “When you were a child your father refused to let you do something you wanted to do. When you asked why you could not do it, his response was simply that he said so. Your repressed resentment of your father makes you hate any arbitrary decision.”

Arbitrary decisions aren’t necessarily bad—sometimes they are necessary. When two parties disagree, they sometimes use arbitration to settle the issue. An unbiased judge, trusted by both sides, makes a decision that he feels is the fairest.

It’s the Rule!

Pedro argues that biological classification is not arbitrary because there are rules determining how living things should be classified. Scientists don’t just assign creatures to various groups on a whim. Therefore classification isn’t arbitrary.

He’s partly right. The assignment of creatures to various groups isn’t arbitrary because it is done according to established rules. We don’t dispute that.

What Pedro fails to recognize is that the classification rules themselves were created arbitrarily, and change arbitrarily.

As Pedro himself said, “At the time of Bakker's publications the prevailing school of systematics was the Darwinian ‘evolutionary systematics’. Nowadays cladistics is regarded as superior to evolutionary systematics.” It was an arbitrary decision to replace evolutionary systematics with cladistics.

Pedro falls into a paradoxical rabbit hole that leads him to conclude that “all birds are reptiles” because “groups are not formed based in similarity, but in relatedness.” It is difficult to measure similarity; but it is impossible to measure relatedness without genealogical documentation.

Imagine three girls, Alice, Betty, and Carol, who are nearly identical. The only differences are that Alice and Betty have blue eyes, but Carol has brown eyes; and Alice and Carol have straight blond hair, but Betty has curly black hair. Which girl, Betty or Carol, is most similar to Alice? What is more important, eye color or hair color? It is an arbitrary decision.

Here’s the harder question: Which girl is most closely related to Alice? If you don’t have any genealogical records, there is no way to tell.

You might think that DNA could be used, but over the years we’ve given many examples from the professional literature where DNA analysis produces results that are counter-intuitive at best (and absolutely ridiculous in some cases).


Pedro says, cladistics is an “unbiased way of classifying organisms.” Let’s start with Webster’s definition of cladistics.

Definition of cladistics
:  a system of biological taxonomy that defines taxa uniquely by shared characteristics not found in ancestral groups and uses inferred evolutionary relationships to arrange taxa in a branching hierarchy such that all members of a given taxon have the same ancestors 3

The foundation of cladistics is biased because it uses an evolutionary assumption! Furthermore,

The outcome of a cladistic analysis is a cladogram – a tree-shaped diagram (dendrogram) that is interpreted to represent the best hypothesis of phylogenetic relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now commonly used in phylogenetic analyses, and the parsimony criterion [that is, the criterion that requires the fewest evolutionary changes] has been abandoned by many phylogeneticists in favor of more "sophisticated" but less parsimonious evolutionary models of character state transformation. Cladists contend that these models are unjustified.

Every cladogram is based on a particular dataset analyzed with a particular method. Datasets are tables consisting of molecular, morphological, ethological and/or other characters and a list of operational taxonomic units (OTUs), which may be genes, individuals, populations, species, or larger taxa that are presumed to be monophyletic and therefore to form, all together, one large clade; phylogenetic analysis infers the branching pattern within that clade. Different datasets and different methods, not to mention violations of the mentioned assumptions, often result in different cladograms. Only scientific investigation can show which is more likely to be correct. 4

In a recent newsletter we showed the diagram below comparing four different avian species trees obtain using different genetic comparisons.

FIG. 4 Species trees inferred from concatenation of different genomic partitions. (A) Intron tree. (B) UCE tree. (C) Exon c12 tree. (D) Exon c123 tree. The tree with the highest likelihood for each ExaML analysis is shown. Color coding of branches and species is as in Fig. 1 and fig. S1. Thick branches denote those present in the ExaML TENT. Numbers give the percent of BS.  5

This “unbiased” method gives different results depending upon which “sophisticated” model you chose, what data points you chose to use, and how you chose to use them. The only way to determine which result is most likely to be correct is to use “scientific investigation” to find the results that agree with your prejudice!

Evolutionary “Truth” Changes

Since science no longer depends on the scientific method (which uses experiments that always give the same results no matter who does the experiment, regardless of the beliefs of the experimenter) to determine truth, evolutionary “truth” changes to suit the prevailing opinions of scientists. Pedro claims, “All science evolves.”

Scientific truth doesn’t change. Newton’s laws of motion aren’t wrong. F = ma is still true. Yes, we have learned more laws of motion for special cases; but what was true in Newton’s day is still true today. Old physics textbooks aren’t wrong.

Old biology textbooks contain facts that are no longer true. Since belief about the metabolism of dinosaurs isn’t based on the scientific method, dinosaurs can be cold-blooded in one textbook, and warm-blooded in another, depending upon the arbitrary declaration of a consensus of scientists. Pedro says this isn’t an opinion—it is an idea supported by several lines of evidence. What’s the difference?

Science has been so corrupted that even professionals confuse speculation with science.

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1 Disclosure, August 2014, “Dinosaur Delusions”
5 Erich D. Jarvis, et al., Science, 12 December 2014, “Whole-genome analyses resolve early branches in the tree of life of modern birds”, pp. 1320-1331,