Adventures with my DNA Barcoder

"But humanity is bioilliterate. Yes, there is a high priest for the name and natural history of some species. That person, however, is almost never standing by your side. But with Google, can you get it? No, there is no hole in your computer or handheld into which to insert the biobit to link through Google. Who is going to give you that name in the dark, the rain, the backyard, or the rain forest? True bioliteracy is being able to link what humanity knows to the biodiversity in hand, eye, or mouth, and build on it. What is the cost to let all seven billion of us read wild biodiversity, now? The barcorder in the back pocket" (Janzen, 2010, Biotropica, 42:540-542).

Thursday, 25th
I am so excited! Today I bought my DNA Barcoder from the gift shop at my local natural history museum. It comes with a two page booklet that tells me I need 6 AAA batteries and something to barcode.

Friday, 26th
I went down to the university to show my new barcoder to my sister. She needs lots of fresh tissue to do her molecular work and always complains that her specimens are either too old or contaminated. "Not with this!" I told her. She looked at me and my barcoder and started laughing. Stuck-up cow.

Saturday, 27th
Today is my first barcoding day (it rained all week, so there was nothing to barcode). I barcoded my cat, which it turns out, is 'human'. Perhaps it's because humans and cats are closely related? Perhaps I need something more distantly related?

Sunday, 28th
I barcoded an ant that I found crawling behind the sofa. The barcoder tells me it's a fungus. I see no other ants. Later on I find a honey bee trapped in my kitchen window. It comes up as a 'geranium'. The barcoder really needs to be calibrated or something.

Wednesday, 1st
Finally, a hot and sunny day! I tried to entice a bird with bread crumbs. No luck.

Thursday, 2nd
Couldn't get close enough to the house sparrows in my park to barcode them. I barcoded various trees in the arboretum. Amazing! The barcoder gets it right every time. There was only one plant sign in the whole park that was wrong!

Sunday, 5th
What a day! Yesterday morning I found a whip snake sunning itself on my porch. I managed to barcode it before it bit me in self defense. Luckily the hospital knew which anti-venom to use because my trusty barcoder got it right again!

Tuesday, 7th
I’m going to be famous! I barcoded a cicada and found that it was 7 different species! I rushed down to the local natural history museum to tell them of the news. Perhaps they can name a news species after me? Apparently the museum barcodes species from all over world and no longer employs taxonomists (the ones who describe new species). A barcoding technician pointed out several local amateur entomological groups I could join. "That's where you find taxonomists now" he said. Perhaps I’ll try Google.

Didn't we discuss this before?

I once walked into my colleague's room and pointed out that his sink was leaking and getting some boxes full of reprints wet. I suggested he should get it fixed or move the boxes. We discussed it a little and after a short while it was forgotten. A year later I noticed that the problem had not been fixed. The reprints were all moldy and the leak had spread staining his carpet. I pointed it out to him again. He simply dismissed it with the line "Didn't we discuss this before?"

That same line is used throughout systematics and biogeography to dismiss lengthy heated debates that never were resolved. Who, for instance, were the victors in the following debates?

Cladistics versus Phenetics

Pattern Cladistics versus Numerical cladistics

Modern Synthesis versus Cladistic Revolution

Dispersal versus vicariance

It is said that history is written by the victors. Looking at the above examples we assume that cladistics triumphed over phenetics (overall similarity); Pattern cladistics simply lost a pointless debate; The Modern Synthesis was expelled from numerical revolution and that the dispersalist have finally won in their campaign against the dusty old vicariance biogeographers. In every case above, a heated debate occurred, the problems were addressed and everyone went home feeling like something was resolved. If this is the case why is vicariance still the most prominent theory in systematic biogeography? Why does everyone use phenetic methods? Where have all the cladists gone?

None of the above debates were resolved. Phenetists kept doing phenetics. The idea of overall similarity (a non-cladistic idea) swept over all of numerical phylogenetics. The pattern cladistics never left, the Modern Synthesis never died and vicariance was never abandoned. If we are to complain that this was all discussed before, then isn't it because the debate never really ended?

In a recent paper all opposition to DNA Barcoding was dismissed has “... having been controversial” (Lahaye et al. 2008). The paper suggests that by doing DNA Barcoding regardless of its flaws, immunizes it from any criticism. I am sure if another paper is published criticizing barcoding it would be dismissed with that one line "Didn't we discuss this before?" This is the same tactic used by phenetists (overall similarity), Modern Synthesists and Dispersal Biogeographers. It seems that history is not written by the victors, but by those with leaky sinks, a stained carpet and no ambition to do anything about it. But surely "we have discussed this before?"

References

Lahaye, R., van der Bank, M. Bogarin, D., Warner, J, Pupulin, F., Gigot, G., Maurin, O.,Duthoit, S., Barraclough, T.G., Savolainen, V. 2008. DNA barcoding the floras of
biodiversity hotspots. PNAS.10.1073/pnas.070993610395.

Abstracting and Seeing – Homology and Similarity

Abstracting and Seeing

Natural Classifications are often discussed as separate issues to our own experiences and observations. Debate rarely touches on the issue of what a natural classification means to a taxonomist or systematist. If natural classifications, like homologies, are supposedly "abstract things" that taxonomists make up in order to make sense of the world, why do we see them? Can we see abstractions or are we doing something else?

Abstractions are hypotheses conjured up in order to formulate a system or artificial "classification" - that is, categorizing things based on a set of subjective rules or characteristics. We may state for instance that anything with six legs is an insect, and so forth. We may view the world through our chosen abstraction and thereby simplify what we are observing. We call this abstracting. It is not observing but simply glancing, looking for particular characteristics rather than observing the whole organism. Artificial classifications are abstractions. An invertebrate, an organism without vertebrae or a spinal column, are unobservable. Reptiles and unicorns are also unobservable but we know what they are and what characteristics define them. Abstracting is not seeing or observing, but simply employing a hypothesis to do the job of "seeing" for you.

Not being able to "see" something does not mean it does not exist. At times artificial classifications contain real (evolutionary) characteristics. Microscopic organisms or electrons too are unobservable to the naked eye, but can be discovered through tools such as microscopes or experimentation. Invertebrates, like reptiles are not only unobservable, they are also undiscoverable.

Seeing is what taxonomists do in order to know an organism. When we see, we do not go through a predefined list of characteristics. Seeing a dog does not make us recite a list of mammalian characteristics. We just see and recognize it. This is what taxonomists do.

Taxa define themselves rather than the other way around. A white blackbird for instance is still a blackbird even if an artificial classification lacks some characteristics or contains a few conflicting ones. An artificial classification for instance may place the American Robin into the Muscicapidae (Old World flycatchers) because they are similar to the European Robin. We can, however, see that the American Robin is the same as a Blackbird, even though they are similar to European Robins. That sameness is a relationship or homology. Natural classifications are defined by homologies rather than the similarities between arbitrary sets of characteristics as in artificial classifications or systems.

The difference between seeing and abstracting is one that divides the biological community. That division runs deep, especially in the case of total similarly versus relationship.

Homology (Relationship) and Phenetics (Similarity)

Homology is about relationship

When the same characteristic manifests itself in other taxa (e.g., a forearm appearing in the wing of a bat), we have found a homologue (sameness). Homology is about the relationships between two homologues when compared to a third (the Cladistic parameter). Homologies are discoverable and tell us that taxa are related.

Phenetics is about similarity.

When a similar characteristic manifests itself in other taxa (e.g., a leaf ratio of 2:3), we have found a similarity. Phenetics is about the overall similarity between two homologues only. Similarities are generated, that is proposed, and predict that taxa may be related based on a measure of confidence.

Homology, then, is evolutionary, as it discovers homology. Phenetics is non-evolutionary as it only predicts degrees of similarity. The differences are evident and should be construed as a negative criticism on our behalf.

Phenetics is simply an artificial classification system. Even though it endeavours to use homologies, it can never discover homologies only propose them. The tools used in phenetics are borrowed from mathematics (statistics) in order to replace what we do naturally, that is observe. In this sense a number of techniques are phenetic. These range from DNA barcoding to Bayesian analysis to cladistic analysis (optimisation etc.). They are based on the fundamental rule of similarity and hierarchy mixed with ad hoc proposition of evolutionary mechanisms, many of which as at best hypothetical.

Homology (monophyly) is a natural classification system. It is a discovery based on sameness and similarity. The tools we use in homology are unsophisticated and at times phenetic (i.e., relying on similarity). Since homology is discoverable and can be observed, taxonomists have been relying on their own intuition to find out what these natural groups are by studying homologies. The same taxonomic method is used today, but is not as thorough as one would hope. Phenetics, however, has helped develop a number of tools that imitate what we do naturally, in order to test whether our groups are truly groups (monophyly). Where our objections lie is how these tools are used. Rather than use phenetic tools to test our hypotheses, many are replacing the practise of testing with observing, without recourse to our own experience. In other words we are allowing algorithms (no matter how good) to do the seeing for us.

All numerical or phenetic methods are secondary to our own knowledge. This should not be interpreted as a Jacobian outburst, but rather as a cautionary statement. Already many systematists are not looking at their organisms and proposing hypotheses of their groups. Instead they are accepting these tests as hypotheses. In our view phenetics, as a system for testing potentially monophyletic taxa, are becoming primary in taxonomy and systematics. This has resulted in non-taxonomic practises to govern taxonomy (i.e., DNA Barcoding, molecular systematics etc.). Our grudge is not against phenetics, a field worthy in its own right, but at those who feel that it is all there is to taxonomy and systematics.

Given the non-evolutionary nature of phenetics, namely its inability to find or even recognize monophyletic groups, why do we need it in systematics and biogeography? Its simplistic aim of proposing similarity is convoluted by numerous algorithms, neither of which advance our field or our knowledge of the natural world. The Great Phenetic Revival returns us to an age old argument fought at the end of the 18th century, namely artificial classifications versus natural classifications. Nothing in our field today has advanced our understanding of classification (i.e., homology and monophyly) since 1858, a point that we will return to later.

The Great Phenetic Revival 3: DNA Barcoding

DNA Barcoding is not often directly associated with phenetics or numerical taxonomy. Given that it is without any methodological or theoretical foundation, DNA Barcoding has very little to with anything associated with taxonomy or comparative biology. Then we happened upon Sokal & Rohlf (1970) The Intelligent Ignoramus, an Experiment in Numerical Taxonomy published in Taxon (19: 305-319).

What is striking about Sokal & Rohlf's "Intelligent Ignorumus" is that it totally undermines our in-built ability to classify, even groups we do not know. Any one from the southern hemisphere would know how to group "Song Birds" based on characters that have not been pointed out to them. It is what we do naturally. Consider the European Robin (Erithacus rubecula), the American Robin (Turdus migratorius) and the European blackbird (Turdus merula). Based on their common names we group them as Blackbird (E. Robin, A. Robin). But if we look at them, it becomes clear that the European Blackbird looks like an American Robin. See for yourself. You don't need a detailed list of pre-defined characters; it is what we do naturally. But Sokal & Rohlf don't think so.

The Intelligent Ignoramus is a simpleton. They are "unprogrammed" with little to no training in biology, meaning the are unable to identify the organisms before them as "bees" and therefore are presumed to lack the ability to classify bees in general. Sokal & Rohlf's test was to assess: "The feasibility of using technicians untrained in taxonomy to collect data for use in numerical taxonomic studies .. [and ] ... the analysis of their descriptions were compared with the data of Michener and Sokal (1957)" (Sokal & Rohlf 1970: 305). The results astounded the authors.

The two technicians managed to find a similar classification of bees. Anyone looking at bees for the 170 hours (as mentioned in the results) would obtain a general knowledge of bee morphology. Obviously this time would be remarkably reduced if a trained taxonomist had pointed out the relevant morphology and the characters that relate various bee groups. Instead of seeing the obvious, Sokal & Rohlf make an enormous blunder. What if the technicians had measured all the specimens, that is quantifying the qualities that helped them group the bees? Quantities can be standardized and therefore automated. In fact, one "... could hire teams of technicians to study the specimens, make the necessary measurements, and record the data and perhaps even select the characters themselves. One step beyond this would be to automate the entire process completely" (Sokal & Rohlf 1970: 318).

The future of taxonomy envisioned by Sokal & Rohlf - groups of "Intelligent Ignoramuses" coding taxa to be processed by numerical methods - is typical of phenetics and their attempts to remove taxonomists from doing what they do best. Now, all of this is starting to sound familiar. "Intelligent Ignoramuses" that can identify and classify taxa without the burden of taxonomic training have reappeared in the guise of DNA Barcoding (identification) and the Phylocode (classification).

Can we re-label DNA Barcoding as Phenetic? Usually phenetic methods or techniques are considered, but rarely do we ever identify phenetic ideas or intentions. The Great Phenetic Revival is the revival not only of phenetic methods but the ideas endorsed by early phenetists like Sokal & Rolf. Read phenetics as Numerical Taxonomy and one quickly realizes that it's about numerical data - quantities, not qualities - and about obtaining such data mechanically and processing it quickly. The taxonomist is not a machine. He or she does not seek to provide measurements. The aim is to discover homologies. The same is true for classifications. They are based on monophyly, not on some general rule of classification. Unfortunately, the Great Phenetic Revival is about the rise of Intelligent Ignoramuses, those that wish to supplant taxonomy and systematics with phenetics under the guise of helping taxonomy. What a frightening thought.