Episode 2: Talkin’ Taxonomy (Charles’s Interests)

Image of a circular phylogenetic tree.

Image: “A phylogenetic tree of life, showing the relationship between species whose genomes had been sequenced as of 2006. The very center represents the last universal ancestor of all life on earth. The different colors represent the three domains of life: pink represents eukaryota (animals, plants and fungi); blue represents bacteria; and green represents archaea. Note the presence of Homo sapiens (humans) second from the rightmost edge of the pink segment.” (Source: Wikimedia Commons)

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Charles: This is Assigned Scientist at Bachelor’s. I’m Charles, and I’m an entomologist.

Tessa: I’m Tessa and I am an astrobiologist

Charles: And today, uh, I thought we would talk about biological classification and the history thereof and controversies thereof. So specifically, I guess, to begin with… how much, like, how much is taxonomy and systematics a part of your awareness of, like, biological diversity…

Tessa: I mean, I know some about it just because of, you know, my schooling and also because of discussions, it comes up in my field periodically when we talk about how do we classify edge cases like viruses, what domain do they fall into? If they fall into a domain, are they alive or not?

I know, at least there’s been one astrobiologist, Peter Ward, who suggested that we, at some point, we’re going to have to come up with a classification category above domain for when we start developing or start discovering like truly extraterrestrial life. But, uh, beyond that, my knowledge is kind of spotty to be perfectly honest.

Charles: Fair enough. So I will say, first off, that the actual parameters of systematics and of taxonomy by themselves and especially relative to each other are often unclear. Well, I tend to define systematics as being about reconstructing evolutionary relationships among groups and taxonomy as being the system that we use to codify those relationships, as well as to assign names and classifications to organisms, uh, so that we can talk about them. So my area of interest is particularly over about the last 50 years, but for a beginning, I’m going to go back too the late 1700s when Carl Linnaeaus, I believe he was a Swedish, um, botanist, he introduced basically the, the binomial nomenclature for biological organisms, where you have a genus name and then a species epithet. People didn’t really accept evolution as the name of the game for about a century afterwards. Like it was about a century between when Systema Naturae was published and when On the Origin of Species was published. Charles Darwin – he didn’t introduce the idea of evolution, his major contribution was providing an explanation for a mechanism driving evolutionary change through natural selection.

Tessa: Right, the actual mechanics of it.

Charles: Yeah, because at that point, people generally had the idea that evolution happened, but there was no accepted explanation for why it happened and how it happened. Evolution has been a hundred percent non-controversial within biology for 150 years. Basically.

So my interest is largely in the nature of scientific biological classification now, because we have the system that has been in use for over… for basically a century before we had natural selection as a concept, and then natural selection came around and it wasn’t for about another century that people understood genetics and genetic inheritance.

The story in biology a lot of the time is of tools and systems that were made before a major discovery, then being retrofitted to suit the new scientific consensus. And so with classification, another major event happened in the 1960s alongside the work of this guy, Willi Hennig. Have you ever heard of Willi Hennig?

Tessa: Probably, but it’s not leaping to my mind at the moment.

Charles: Fair enough. So Hennig was, um, an entomologist. Hennig came in with the idea of cladistics where… cladistics is the idea that these classifications of organisms should be based on an evolutionary relatedness, where we shouldn’t just put two things together because they are more similar to each other than they are to anything else, we should put them together because that classification encodes our understanding of evolutionary relationships between the two. One of the major ideas here is of, uh, monophyly, where that’s a term that basically means a group as defined by including their most common ancestor and all of the descendants of that ancestor.

Then this introduced the idea that classifications should only be made – like a named group should only be a monophyletic clade. Clade, cladistics. There you go. A major simplification, but this has been essentially the consensus position for about the past 50 years, the idea that we should be grouping things together so that they reflect these monophyletic clades in the history of life.

Alongside monophyly there’s also paraphyly and polyphyly. Paraphyly is a group that is defined as including the most common ancestor, and many of its descendants, but excluding some of them so that it doesn’t get the whole group all in one. My particular interest as an academic and as somebody who loves taxonomy and as somebody who loves a group called Dictyoptera is in the treatment of paraphyletic groups, and this impulse that the only valid names and only valid groupings are ones that are monophyletic, and particularly, this is interesting to me in a pretty recent phenomenon known as the PhyloCode.

So backing up two steps… most naming for the past a hundred years in biological organisms have been governed by nomenclatural codes published by professional societies. So if you want to name a new animal, you have to do it according to the rules of the Zoological Code of Nomenclature. These codes typically only govern genus and species. Any higher ranks are only going earned by them insofar as they need to have certain endings.

So in the Zoological Code of Nomenclature, if you want to name a family, it has to end with I-D-A-E, or “-idae.” But other than that, the actual content of the names and the meaning of those ranks is not really governed by the nomenclatural codes.

Tessa: So basically as long as you have the right, like suffix or ending on it, you can call it whatever you want.

Charles: Basically. Historically these higher ranks have been largely unregulated in a major way. And they in particular, much more than genus or species, fall into this issue of practical paraphylies. Just based on who uses these rankings, who makes these rankings, how long these rankings have gone unrevised or unchallenged or unexamined.

A lot of times you have these ranks that, functionally speaking, are not monophyletic, but because they work and because nobody is challenging them, they remain in the classification. One thing that is fascinating to me is this phenomenon of something called the PhyloCode.

And so the PhyloCode basically was introduced around the millennium by basically these two guys who looked at the classification system and the naming system, and they said, this won’t do, a lot of this is not informed by evolution in any meaningful way – you got paraphylies, you got polyphylies, God forbid. Um, and all of these higher ranks are largely just issues of like practical naming rather than evolutionary naming in a true sense. Just recently, like a month ago, they published the first actual edition and I am dying because Arizona State does not have institutional access and the e-book costs $50 and I’m a grad student and I don’t have $50 to spend on a, probably barely updated version of something for which there are four free versions, but I want to read it so much.

 So June 8th, 2020, on the Florida… University of Florida, Florida museum website, new books present the PhyloCode and evolution based system for naming organisms. It literally begins with, “Move over Linnaeus, there’s a new way of naming organisms.”

Tessa: That’s pretty bold.

Charles: It’s extremely bold, especially because, so we call it the Linnaean system of classification. but in reality, it’s a lot like calling our contemporary understanding of evolution Darwinian. Darwin died like 120 years ago, scientific inquiry didn’t. Like Darwin died before anybody knew what a gene was. Right. Like he had never even heard of DNA. He had to posit a theoretical unit of inheritance, but he didn’t live to see the reality of what that unit of inheritance is. And so similarly, calling our system of classification with the hierarchy and with the different ranks that we name things with and with binomial nomenclature “Linnaean” is simplified at best and wrong at worst because it doesn’t represent the literally centuries of thoughts has gone into how we classify and name things since Linnaeus was on the scene and exerting his influence and particularly like Linnaeus didn’t really know about evolution, he certainly didn’t know about natural selection, he definitely didn’t know about DNA. And the retrofitting of evolutionary understandings onto our classification of organisms literally didn’t really come about until the past 50 years of time when Linnaeus was just a skeleton in the dirt. In that way, calling it Linnaean classification is wrong.

So let me describe my understanding of what the PhyloCode actually is and what it’s trying to do. So the PhyloCode was introduced like 20 years ago as basically, instead of taking this long legacy classification system, the traditional classification system often known as the Linnaean system, and trying to squeeze evolutionary understanding in, into it, which is, has been a very messy affair and results in a lot of renaming things, demoting things, promoting things, moving them around.

It’s been very confusing, especially because another aspect of why taxonomy… has been sort of the wild west of fantasy in terms of, um, governing and naming different things and moving things around is because there are so many people and there’s no centralized authority on names, basically.

The PhyloCode is saying, instead of trying to retrofit this legacy system that came about before people even broadly accepted evolution as an idea, why don’t we create from the ground up the classification system, which is specifically, exclusively, explicitly evolutionary in concept and in execution.

In systematics, our primary sort of export to the world is in the creation of phylogenetic trees. If you’ve ever seen an illustration of like the tree of life, you have seen a phylogenetic tree, probably if you have only seen it in that context, it has been a literal tree. Our main export to the world as as systematists is the creation of these phylogenies, which is basically like you have the starting point and then you have these nodes, which are branching points. And then every branching point, every node represents an ancestor, a shared ancestor, and then the branches away from that node represent the different paths of lineages.

So let’s say that you had, you have the common ancestor and then you have these branching points and then the branching points branch and they branch, and they branch and they branch until you get to terminal taxa and terminal taxa are the ones that haven’t branched out into anything more, they’re the ones that are extant in the world now.

And so the PhyloCode is basically saying instead of having this phylogeny and then trying to squeeze it into the structure that we already have, in, you know, sort of our traditional classification, why don’t we just take the tree and we attach names to this tree as it is. Like that node – now that is, that is a clade that has a name.

What is interesting about this is that it’s, well, a lot of things, but the thing that always strikes me the most is the notion that this is a viable option given the contemporary status of our understanding of phylogenies because… well, so there’s sort of two there’s sort of conflicting desires and uses of classifications.

So there’s sort of the need from externally – taxonomy is fundamentally meant to be used. We name things so that we can talk about them. And so from that perspective, there is the need for taxonomic stability, for names to retain their meaning over time, so that if you talk about, so if that, if I talk about something now it’s going to mean the same thing that it meant 50 years ago and it’s going to mean the same thing in 50 years.

But, now that we try to attach evolutionary information to naming. There is the tension there of also naming needing names to be evolutionarily meaningful and informative. And based on that we need them to reflect phylogenies. But the problem is that the phylogenies that we construct keep changing and being refined as we add more and more information.

Tessa: Right.

Charles: And so what is interesting to me, and the first thing that comes to mind is those weird Speedos for people who have penises, where it only loops over like one leg. And I think about- are you familiar with the Try Guys?

Tessa: Uh, yes. Yes, I am

Charles: One of their early videos was like, guys try on weird swimsuits or something.

And one of them said in response, they tried on one of these Speedos, looping over one leg. And one of them in response said, this is relying on the penis to stay in place, but the penis itself is an elastic element, it’s moving around. And I think about that whenever I think of like the PhyloCode and specifically of attaching names to nodes in phylogenies…

Tessa: That is the best analogy for the problems of trying to deal with a fluid and often changing field I have ever heard.

Charles: Thank you so much. I’m quite proud because that’s the thing, is that… it’s always interesting to look at the backgrounds of people who are advocating for these things because often – not always, but often – they are attached to vertebrate groups where broadly speaking, we feel like… globally, I’m saying we just a universal, we, we often feel like we basically know the vertebrates that we have, you know, you get a couple new vertebrates a year and we should definitely at a different time talk about sort of the politics and philosophy of scientific “discovery” of species, because it’s definitely weirdly colonial and we should get into that, but for our purposes when we’re talking about discovery, as in like, Discovery to the quote unquote scientific community and giving it a binomial name and slotting it into the literature you get maybe a couple new vertebrates a year. Maybe, and a lot of the time, those are even things that aren’t like, we went out into the rain forest and we saw a new frog, it’s we previously grouped all of these frogs together and then we looked at them more closely and we decided that actually they should be two species.

Whereas in entomology, even putting aside any other invertebrate groups, there are so many insects. There are a lot of insects. There are a couple of groups whose like higher level phylogeny seems pretty solid, and we generally seem to think that like the higher, higher of phylogeny of like order level phylogeny of insects is pretty good. We feel fairly confident about that one.

But for instance, there have been a handful of a major phylogenies published of Blattodea, which as an order now includes cockroaches and termites. There have been a handful of those published over the past several years. And the level of agreement between them is very small. And so if we were going to take any one of those and attach names to the nodes that are turned up in those phylogenies, those names would be functionally inert basically for a while, because our understanding of that phylogeny just as, is not at a point where, as far as I know, anybody is actually going to say, yeah, this is definitely, definitely, definitely the way that it goes.

There are a couple groups within Blattodea that we feel very confident about being related, like termites as a whole are a sister group to Cryptoceridae. We feel good about that, but there’s just there hasn’t been… cause that’s the other thing also in entomology, particularly if you look for systematics labs and entomology, most of the time it’s going to be like ants, beetles, more ants, different beetles. Lepidoptera maybe, um, we got a bunch of fly people – they’re mostly in Brachycera, mostly in Schizophora. And then the rest of it is sort of, you have maybe a couple dedicated labs per order. And that’s basically it. So there’s the double issues both of, we definitely haven’t documented every insect species in the world – and the really depressing reality is that probably a lot of species will have risen and fallen into extinction before anybody ever gets to see them with our human eyes.

Tessa: So basically what we’re facing is that we’re trying to build like a universal system of classification organization but with the knowledge we have from that only very, very partial about the organisms we’re trying to classify.

Charles: Yeah. And the other thing that gets me is that a phylogeny is always a simplification. Inevitably. A phylogenetic tree cannot capture the full complexity of evolutionary history by its very nature. So in a lot of different ways, and particularly in when you build a phylogeny, there is discrimination built in from the beginning if you’re working in any group bigger than like… Theoretically, if you wanted to do a phylogeny of all cats, you could probably get samples from every cat, because there were only like 36 species of cats. From an entomologist’s perspective, 36 is nothing. So you could do like all cats, but even the family that I did my thesis on is considered a pretty small family of flies. It has over 500 different described species.

Tessa: Good Lord.

Charles: Yeah. And a lot of these species are known from essentially a singular type specimen in one museum collection. So if you, for instance, if you’re doing molecular systematics where you’re using DNA, you fundamentally cannot do, even if you had every single species, like as it’s known to people, you couldn’t do a molecular systematic phylogeny of all 500 plus species of  Ulidiidae without going and doing extremely huge, detailed collection to find new samples of certain species, because like… the guy who runs the museum, I think in Philadelphia, the insect museum that has the single type specimen of like Hiatus fulvipes, they’re not going to give it to you so that you can crush it up to get DNA. Cause then whoops, your DNA extraction didn’t work and you just destroyed literally the only specimen of this species that anybody is known to have.

Tessa: Oh dear.

Charles: Great job. So they’re… like, you can’t do that. And so what always strikes me here is that all insect phylogenies by their nature are discriminatory in their selection of representatives because it is a logistical impossibility to be exhaustive. And so because of that, a phylogeny, so, and also systematics is kind of a weird field in science because a lot of what we do, and we talked about this last week, a little bit in talking about what you do in astrobiology, a lot of what we do in systematics is fundamentally unprovable and unfalsifiable, because we lack the ability to go back in time and actually document the full spectrum of exactly which species diverged at which points, especially because a divergence point in your mind might be, well – there was one day and then these two rabbits were in a valley together, and then whoops, there was an avalanche and they were separated and then thereafter, they were separate species, sort of like a classic example from undergrad evolutionary biology courses. But the reality is that speciation is an extremely weird erratic, gradual, non generalizable phenomenon across time. Like, there’s just no way for, unless we literally all became God, we can’t look at our phylogenies and say with absolute certainty, which is right, and which is wrong.

Tessa: Right.

Charles: There is underlying a lot of support for phylogenetic nomenclature, as well as monophyly-exclusive building of classifications relies on this belief that there is fundamentally a right phylogeny and that as we progress forward with the tools that we have now that we have not only morphological evidence, but molecular evidence, et cetera, et cetera, we can progress forward to a point where we have either a right phylogeny or as close as we’re ever going to get.

And as an entomologist, as well as a skeptical pessimist by nature, I am unconvinced that that is a reality that most of us are going to see at least in our lifetimes and/or before total cultural collapse into climate change apocalypse, you know, either.

Tessa: Whichever comes first, you know.

Charles: Whichever comes first, basically… PhyloCode is, is fascinating to me partially because it has not really because it’s, you know, it’s been available in some form or another for… basically two decades that hasn’t, and it hasn’t really been taken up by people outside of the people who were already advocating for it. Like, it hasn’t really changed the way that people actually have been doing taxonomy. And so it will be interesting to see if now that they have like an official first edition, whether that changes, and a lot of the underlying claims of the PhyloCode and a phylogenetic nomenclature also… because I think the people who are behind PhyloCode and me are on sort of separate ends of a spectrum of realism versus practicality, or I guess realism and practicality are sort of united here, but so practicality versus, I don’t want to say ideological purity because that’s weird, but this sort of like…

I tend more towards practical… of like, even like holistically in terms of like how I understand science and why and how we do science, of being like, true objectivity is impossible. Everybody gets coming in with a perspective, getting to some sort of… an absolute truth that probably exists, but it is fundamentally and accessible from within a human brain versus people who are more like, we have to have monophyly-exclusive classification, or at least as close to it as possible because to do otherwise is to sacrifice scientific rigor for the benefits of shortsighted practicality, which is maybe a harsh way to put it, but that’s kind of, you know, that general area.

Tessa: Yeah. That makes sense.

Charles: Yeah. And so that’s basically what I wanted to say. Um, I love… cause I love taxonomy and I love classification. And I, I was reading a paper last night… this is what we’ll end on. I was reading a paper from the late nineties, which was fascinating because, technically, molecular systematics had become available by that point.

Like theoretically, it had become available way earlier when like PCR, you know what PCR is, right?

Tessa: Oh yeah.

Charles: Yeah. For anybody who doesn’t know PCR is stands for polymerase chain reaction. And it was basically a tool that was developed that allowed people to get many more copies of DNA that they had been able to previously.

And so molecular systematics basically is systematics, it’s building phylogenies using molecular data. So DNA, RNA, that area of things. And so reading papers about systematics from the nineties is fascinating because they are at a point where molecular systematics is essentially available, but it isn’t really widespread yet.

And in particular, like the major molecular systematics papers that were published in the early 2000s largely use a couple of individual genes versus now we have, phylogenomics where you sequence the whole genome of an organism and then compare those and the technological turnaround on that is like 15 years, we’ve gone from three genes to a genome, which is incredible. And then phylogenomics and the age of phylogenomics brings up its own issues with like abundance of data and how much of it is actually useful versus how much of it is just random, garbage that is noise, like et cetera, et cetera. But we’re not talking about that today and we should stop talking in general cause I’ve been talking for a very long time, but essentially. Taxonomy is the best. Insects are the best. Phylogenetic nomenclature… remains to be seen.

Tessa: Yeah, I think I agree. I think that’s a good note to end on that, you know, we have these brand new, well, maybe not all that new ways of thinking about it, but we it’s still gonna be an open question of whether or not it actually accomplishes what it intends to.

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