How Far We’ve Come: a case study in arthropods

Well, I’m into my second semester of graduate student life, and excited that my research is finally starting to get somewhere. Maybe. In theory.

I feel compelled to write about something I’ve noticed lately: science moves really fast. True, this may not come as a surprise to some of you, or even most of you. Maybe it’s because of my age, but even though I conceptually knew that science moves at a quick clip, it took a personal insight for me to really feel it. What follows a bit of a departure from my usual science-only schtick (I promise, there IS science here… it just needs an introduction, in the form of a grad school anecdote.)

All of the first year students in my department are required to take a course that meets weekly from 5 – 7 PM on Wednesdays. Although initially this served as a convenient means of getting to know each other and the faculty, now it just seems like a time sink. (I’d prefer to eat dinner instead.) Given my short attention span and general ornery demeanor on weeknight evenings, I did not expect to feel any sort of vast change in perspective in this class. So you can imagine my surprise when I did.

In lieu of remaining faculty to introduce ourselves to, the cohort has been discussing Steven Jay Gould’s book Wonderful Life: The Burgess Shale and the Nature of History. The details of the Burgess Shale may need to wait for another day–though it is a story worth telling (and perhaps not in Gould’s verbose style…)–but the book makes use of a staple of invertebrate biology: the arthropod family tree, formally called the phylogeny. That is where my real story begins.

The arthropods are the most numerous animals on the planet. Insects, crustaceans, spiders, horseshoe crabs, centipedes, millipedes, extinct trilobites, and assorted other creepy crawlies all fall into this gigantic phylum.

Recursive arthropods! A harvestman (Opiliones) with mite (Acari) parasites
It's an arthropod eat arthropod world. Recursive arthropods! Here is a daddy-long-legs (a.k.a. harvestman) (Opiliones) with mite (Acari) parasites.

When Gould published his book, (the year I was born, as it turns out), the arthropod phylogeny was not well established, but the subgroups of arthropods were. The major  groupings (I’ve omitted many smaller ones) looked something like this:

Once upon an out-dated time... insects were most closely related to centipedes and millipedes.
Once upon an out-dated time... insects were most closely related to centipedes and millipedes. There are others, but I'm lazy.

It was a fact. Insects were part of the group Uniramia with centipedes and millipedes. Crustaceans were a separate group.

Fast forward 22 years. At least one nerdy kid turned into a graduate student in evolutionary biology. There have been over seven generations of Game Boy. And insects are crustaceans.

What? Yes, you read that correctly. Even though Steven Jay Gould was absolutely confident in his declaration that insects were in a group with centipedes, (Uniramia) molecular evidence places insects WITHIN the Crustacea. And Uniramia doesn’t exist. Millipedes and centipedes are now in a group called Myriapoda.

Arthropod classification, nesting insects within crustaceans
With new molecular data, we are fairly confident that Crustaceans and Myriapods are sister taxa, and insects are within the crustaceans.

But how could Gould have ever known? Most of the morphological evidence seemed to place insects away from crustaceans, in with centipedes and millipedes. They have different breathing structures (insects and centipedes have tracheae as opposed to crustacean gills). They have different limbs (crustaceans have biramous, two-branched limbs; insects and centipedes have uniramous limbs). Gould was partly right– it IS hard to pair insects with crustaceans on the basis of anatomy alone. By the late 1990s people began to suspect that the features linking the group Uniramia may have had multiple origins, but no one thought insects were nested within Crustacea. It’s taken a large body of molecular genetics research to start changing the accepted relationships among arthropods.

Of course, the first mention of the keyword “molecular genetics” that I can find in the Web of Science database was a paper by Linus Pauling in 1956. The idea of using molecules to find evolutionary relationships was initially proposed by Francis Crick in 1958, but wasn’t formally suggested until Emil Zuckerkandl and Linus Pauling published the idea in 1965. Willi Hennig’s foundational Phylogenetic Systematics, published first in 1969, doesn’t even really consider genetic methods for tree construction. Biologists created phylogenetic trees using protein sequences as early as 1967 before using genes, but even proteins were not used broadly until some time later.

In fact, it seems that molecular phylogenies were not commonly made or used until the 1990s–after Gould researched and published Wonderful Life. This is not entirely surprising. Polymerase chain reaction (PCR), a technique used to increase the quantity of DNA available for analysis, wasn’t invented until 1983–and was modified and improved through the 80s. (The process continues to this very day, making sequencing and amplification cheaper and faster). PCR was not a common procedure until the early 1990s. The molecular phylogenetic trees we see everywhere now were not  available to Gould and his colleagues while he was writing; leaving them with only morphological, physiological, ecological, and behavioral traits to build their arthropod tree. No wonder they grouped insects with centipedes instead of crustaceans.

It thrills me to think of how much biology has grown in the past 30 years. Genetics has opened up a whole new world of questions, and new approaches to old ones. As much as Gould tends to decry technology’s ability to advance science, that this revolution happened over only 30 years is amazing. I can’t think of a single branch of biology that hasn’t been affected. And I don’t even use genetic methods myself.

So I find myself wondering:  What’s going to happen in the next 30 years? How many of the things that we “know” now will change? Or be overturned completely? How many new things will we uncover? It’s a good time to be a scientist. If this much has happened in my lifetime thus far, I can’t wait to see what comes next.

______________________________

Many thanks to my brilliant friend and colleague Bruno de Medeiros for sharing his insights on the history of the arthropod phylogeny, and providing comments on an early draft of this post.

The old phylogenetic classifications here I adapted from:
Erwin, DH. (1991) Metazoan phylogeny and the Cambrian radiation. Trends Ecol. Evol. 6: 131-134.

The new classification comes from an incredibly thorough phylogeny of extant arthropods:
Reiger, JC. et al. (2010) Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature. 463: 1079-1083.

** I added in trilobites as an unresolved group, because we’re lacking in arthropod phylogenies including both living and extinct groups.

Some of the history of PCR I learned from this paper:
Bartlett, JMS and Stirling D. (2003) A short history of the polymerase chain reaction. Method. Mol. Biol. 226: 3-6.

Author: Kara

PhD student studying integrative biology, specifically evolutionary biomechanics.

7 thoughts on “How Far We’ve Come: a case study in arthropods”

  1. being a non-scientist, it fascinates and thrills me to read your scientific blog entries. i try to understand whatever i can and look up whatever i can’t. by the time i reach the end, i’ve learned something new, of which i have no prior knowledge (duh!). not something that applies to my life but tapping into different areas and picking up new information is always good. however, being a non-scientist, i enjoy the “human” elements of the entry and tend to focus more on different elements than the scientific ones, such as what is the name and subject of this required, yet time-sinky course? is the class’s focus learning stuff from all the different faculty members or just meeting them and finding out what fuels their fire? and the “cohort” you mentioned – is it a colleague? or the course professor? or a new faculty member you’ve met? is this course led or taught by a different faculty member each meeting or is there a single professor that guides the class through its paces? sorry my comments aren’t scientific, but i guess understanding this stuff helps me appreciate the scientific stuff you impart later in the entry. thanks.

    1. Hi! I’m glad you get something out of the posts, even without being overly science-y. I didn’t include the name of the course because it includes the name of my department; but it’s along the lines of “Topics in __[non-cellular] biology___”. We typically just refer to it by its course number. The focus of the class was a little of both of the things you mentioned–it was more a “get to know your department” survey; but now we’re mostly focusing on our book discussion. No one leads the class. At the beginning, different professors were invited to chat with us, basically. Now we manage our own discussion.

      “Cohort” is the term used to refer to a group of graduate students starting in the same year. All of the first-year graduate students in my department comprise my cohort. The word “cohort” in this case actually comes from a technique used in ecological research, called the life table. These tables trace the survivorship of each group of animals in a population born each year. For instance, one study traced all of the red deer born in a region over many years to see their survival over time. In this case, all of the deer born in year x make up a cohort, year y has a cohort, etc. The life table shows how much of each cohort survives over time.

      I guess that makes “cohort” a very fitting name for a group of biology graduate students who come into a program at the same time.

    1. Yes. They’re most closely related to the formerly considered primitive Remipedia in the crustaceans. At least, that’s the relationship suggested by the most recent phylogenies.

  2. Hi, thanks for an interesting an insightful post. I have long enjoyed Gould’s writing myself, and try to keep his clear, lucid style in mind when I write my own history of science, whether it be for for my blog (which I would invite you over to peruse if you’re interested in the history of science and technology) or for something more academic. He had a way of educating about complex topics in a very straightforward way, which I feel demonstrated not only a deep understanding of his subject matter, but also a profound understanding of people. He did some interesting history of science too; I thoroughly enjoyed his ‘Knight takes Bishop?’ and ‘Fleeming Jenkin Revisited’, both in Bully for Brontosaurus.

    A couple of points came to me while reading this. Firstly, regarding the relationship between science and technology (when the two can be so distinctly defined, which is less frequently than you might think nowadays), it has often been the case that technology gives science something which allows it to advance (although more on notions of scientific progress below), whether it be equipment and apparatus, which has often been conceived without specific scientific training or knowledge, but rather with the technical expertise or trial and error methods of the artisan (steam engines are a classic case study), or a metaphor which provides an entirely new way of looking at and explaining the world (consider for example the mechanical philosophy of the seventeenth century, or the conceptions of the brain taken from developments in telecommunications from the nineteenth century onwards).

    Secondly, regarding the notion of progress within science, this is an interesting topic debated amongst historians of science, and I was wondering if you thought what you are pointing out, which is obviously a change in knowledge and understanding over time, could accurately be called ‘progress’? I recently read an interesting blog post about this by the curator of the history of science and technology at the Royal Observatory, Greenwich which I’d like to draw your attention to: http://teleskopos.wordpress.com/2012/02/08/a-conversation-about-science-and-progress/ I’d be interested to hear your thoughts on this.

    Thanks again for a thought-provoking post!

    Michael.

    1. Hi Michael,

      Thanks for reading. “Interesting and insightful” is high praise! I’d agree, Gould’s explanations are very clear, though there are times when I wish he would make his point a bit more quickly. I’ll have to take a look at Bully for Brontosaurus; I might prefer SJG in essay form.

      I hadn’t thought much about the interplay between our metaphorical appreciation of and technological approaches to understanding the world. Most of the thinking I have done in that arena has to do with microscopes and optics in general. By changing our literal ability to see, microscopes and telescopes, in my mind, really opened up the natural world to analysis… perhaps in ways parallel to our understanding of the genetic code. Apparently, the push by scientists for better optics actually pushed the artisinal craft of glasswork and lensmaking, too. But you probably know more about this than I do! The closest I’ve gotten to historical scientific instruments was a small selection of bronze/metal pieces from my university’s collection. I’m definitely going to read up on your suggestions when I find the time; I enjoy thinking about these topics, but I get caught up in my research. (Also, your blog is awesome. Thank you for sending it my way!)

      Now, regarding progress, it’s been a few years since I seriously contemplated the nature of progress in science, but here’s my take. Science progresses, but defining the nature of that progress is hard. Maybe approaching “truth” is one way of looking at it, but knowing what’s true is hard. One way I conceive of scientific progress is expanding the things we’re even capable of knowing; at least, that’s the kind of progress that’s most exciting (and sadly, the sort I’m least likely to make in my own career). Forgive me if I use a mathematical explanation for this, but I think in terms of spatial dimensions and graphs, so that’s easier for me. Suppose there’s some N-dimensional space that represents all of the things humans are capable of questioning in the natural world at this instant in time. I specify questioning, because I think that’s really the essence of the process, searching for answers to questions that inevitably lead to more questions. To me, progress is the expansion of that space. Anything that lets us go beyond the boundaries of our previous understanding. (I suppose that implies that the understanding is in the “right” direction with regard to truth, but for the sake of brevity/my sanity this morning, let’s not go there right now.)

      I know it seems like my view is biased towards entirely new findings, new methodology, etc. (Again, things I probably won’t do…) But there’s room for puzzle-solving science in there too. For instance, the new arthropod phylogeny is a restructuring of the old phylogeny, right? BUT — it opens up Arthropoda to whole new questions. How did insects move to land? Why are there (essentially) none remaining in marine environments? Are there transitional taxa? I may not be explaining exactly what’s going on in my brain right now very well, but that’s the essence of it. I also think this expansion of “understanding-space”, to continue my mathematical metaphor, is certainly not uniform, nor is it uni-directional per say. You can expand along any axis, right? In fact, I think if you were to collapse part of understanding-space (if we found something were completely incorrect), it would necessitate an expansion in another area of understanding-space.

      Wow, I’ve written a novel. I hope this answers your question as to my thoughts on the matter of scientific progress. I’d love hearing your opinions–perhaps send me an email?

      Cheers,
      K

  3. Thanks, glad you enjoyed my blog, ‘awesome’ is very high praise! I believe the desire of natural philosophers for improved optical instruments probably did help lens-making techniques, but before the sciences recognised the utility of these lens, they would have been developing without any specific, specialised knowledge of the science of light. My understanding is that a lot of this knowledge came about as a result of, and was catalysed by, the availability of lenses. I should look into the history of spectacles and monocles as vision aids, because I can imagine this pressing practical need could have sparked off an earlier interest in producing good lenses, even without the science behind it. Alternatively, the impetus could have been generated by observations of the effects on light of glass objects made as pieces of art, especially by the expert glass blowers of Murano, an island off Venice. Such factors tend to influence one another in interesting and complex ways.

    Your conception of axes is interesting; I like the idea that changes in scientific knowledge over time lead to an increase in that which we can question. However, I would finesse the point somewhat, and say that what is happening is an expansion of the realm in which a naturalistic explanation can be sought and obtained. The more we know the more we can question. However, there is another, less deterministic factor involved, which is our desire to find naturalistic explanations in the first place, as opposed for example to mythical or divine explanations. This is contingent, not necessary. Surely we could always ask such questions, had they occurred to us, but we would not always have asked them in ways which would have led to more similar questions. Rather they may have led us to other types of questions, for example theological, or introspective. These I believe are also useful, but lie within a different sphere of knowledge.

    Regarding the ‘truth’ of scientific knowledge, this is something which is much debated by philosophers of science, and two camps exist, the realists and the anti-realists, who can usually do nothing to convince each other of their own point of view. One problem with talking about truths in science, the anti-realists can say, is that our proofs can be circular: we say that we know something is true, because we can show that it works. But we explain the fact that it works in the first place by recourse to the belief that it is true. This is a little problematic, not least because the history of science shows us that our theories do not necessarily need to be correct in order to work in certain circumstances. At the end of the day I view the solution to this question as being more one of metaphysical beliefs about the outside world than anything else.

    And there’s my novel.

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