Living jellyfish =/= earliest stage in metazoan evolution…

So, admittedly, I wasn’t interested enough in Bielecki et al. (2013) to read the whole thing. But if the abstract is an accurate reflection of their reasoning, then “WTF” is an accurate reflection of my reaction.

The reason I went to have a look at this shiny new PLoS paper is that it was titled “Fixational Eye Movements in the Earliest Stage of Metazoan Evolution”. Anything to do with early metazoan evolution automatically interests me, plus my immediate reaction was to ask how the hell they discovered any kind of eye movement in the earliest animals (which have been, you know, dead for like 600 million years).

Turns out they didn’t. Turns out all they found was that the rhythmic contraction of a box jelly‘s bell keeps the image in its eyes changing so they don’t go blind from photoreceptor fatigue. We accomplish the same effect by constantly moving our eyes (though apparently that’s more for the brain getting bored than photoreceptors burning out?), but the jellies supposedly don’t have the same level of nervous and muscular control over their eyeballs.

Yes, box jellies have frickin’ amazing eyes, complete with lenses. In fact, they have 4 sets of 6 eyes, two of the six being proper camera eyes and the other four much simpler. They can use their eyes to navigate around obstacles and stuff. They are pretty cool creatures. Here’s a box jelly eye cluster (rhopalium) in its full glory from the UCMP:

(Was that just a little bit unsettling? :D)

But these complex, image-forming eyes are an innovation of box jellies. No other cnidarian – in fact, no other animal outside the Bilateria – has them. So complex eyes and good vision are examples of convergent (or should I say parallel?*) evolution, not inheritance from a common ancestor. Conversely, bilaterians don’t have bells like jellyfish, so anything they do to move their eyes has to be an independent invention from the get-go.

So, while box jellies are awesome and it’s always cool to learn more about them, I’m not sure what profound insight about animal evolution we are supposed to find here. That animals with eyes have ways of avoiding visual fatigue? Well, duh. Of course they would, it’s really useful. But I’m not even sure the pulsation of a jellyfish should be regarded as a vision-enhancing adaptation, never mind an adaptation with any relation to what we do. To me it seems like the default way a jelly moves just happens to be good at keeping its eyes entertained. Evolution doesn’t have to do anything special about it.

Of course, the whole thing is soaked with that grandmother of evolutionary misconceptions, exemplified by this quote from the introduction:

Cnidarians were the first of the extant metazoan phyla to develop a nervous system which is therefore considered close to the evolutionary origin of all nervous systems [9].

Nooooooo, for the love of hungry anomalocaridids, don’t do this to me.

Cnidarians and bilaterians shared a common ancestor with a nervous system. Never mind “phyla” – phyla are arbitrary lines humans drew around the branches of the phylogenetic tree. Our ancestors and theirs had nervous systems for the exact same length of time. Neither of us was “first”. Life is a tree, not a goddamned ladder.

Well, at least we got to look at some disembodied jellyfish eyes. Yay!

*goes away to growl quietly*

***

*The difference being that parallel evolution is convergence  from a common starting point. While complex eyes are clearly later inventions, the common ancestor of cnidarians and bilaterians might well have possessed simple eyespots of some sort, providing said common starting point. But we’re getting pedantic here.

***

Reference:

Bielecki J et al. (2013) Fixational eye movements in the earliest stage of metazoan evolution. PLoS ONE 8:e66442

For fuck’s sake, scientists!

Damn. Mistaking evolution for a ladder with us on top is something I fully expect from people who don’t study it for a living, but when evolutionary scientists make that mistake, it drives me apeshit. And they do it all the fucking time.

I don’t think most of them are aware of it. You’ve got to be really watching for the trap to have a chance of avoiding it. I slip every now and then, and then I spot it and rage at myself and get deeply philosophical about human nature and such. It’s such an easy and convenient thing to do. (Think of evolution as a ladder, not get philosophical, I mean.) It’s the way we’ve been conditioned to think since the first time we heard about evolution.

For most of the history of biology, no one blinked twice if you talked with culturally sanctioned anthropocentrism about “lower animals” or “higher vertebrates”. Evolution was a highway of progress, and some creatures just got further along than others. Naturally, we were speeding along right at the front.

Nowadays, I think most biologists who have to consider evolution in their work would tell you that evolution doesn’t work like that. The papers I read rarely contain such explicit references to the “march of progress”. (Can I call it the MOP?) However, that doesn’t mean the references are gone. They’ve just become so subtle that, I suspect, not even the people who make them realise they’re there.

It’s “basal lineages”. “Phylogenetically more primitive” creatures. Or “early-branching organisms”. Or “evolutionary old animals”. All of these are real terms used in real papers published this year. They aren’t restricted to bad papers. And if you stop to think about it, none of them make any goddamned sense.

Let’s picture an evolutionary tree first. I can’t really use my usual tree with all its question marks, but the one below, which I nicked from Srivastava et al. (2008), will do:

srivastava_fig2_183mm

(The species from top to bottom are: brewer’s yeast, a choanoflagellate, this tentacled little guy, a sea anemone, humans, a limpet, everyone’s favourite fruit fly, the Blob, and a sponge.)

The “base” of the tree is to the left, where animals, Monosiga and fungi have their last common ancestor. (That was a long time ago.) “Basal” means close to the base. The branching point (node) that separates animals from the non-animals at the top is the basalmost node in this tree. The node that separates the sponge from the other animals is also a pretty basal node. The creature that gave rise to both sponges and other animals was a truly basal animal.

Now, which is the basal lineage?

The correct answer is “relative to what?”

Every node divides the tree into two lineages. It doesn’t make any sense to say that one of them is more basal than the other. There’s a basal node in the tree of animals. Sponges are on one side of that, the rest of the animals are on the other. If you take a vertebrate species, sponges are the last animal lineage you’ll encounter if you trace its ancestry back towards the base of the tree. If you take a sponge species, the lineage with vertebrates (and lots of other things) on it will be the last.

Basal lineage” depends on your point of view.

Maybe actually taking the sponge point of view will help illustrate this. This tree comes from a paper about sponges (Sperling et al., 2010):

SperlingSponges

Unlike the previous tree, its branches are labelled with larger groups rather than species, but these represent more or less the same range of creatures. Monosiga from tree one is a choanoflagellate. Amphimedon is a haplosclerid demosponge, on the second branch from the bottom. Every other animal from the first tree is compressed down into that one branch labelled “Eumetazoans”. (OK, Trichoplax is not a eumetazoan, but that’s a technicality that doesn’t affect the point.) From this angle, it’s rather harder to see sponges as a basal animal lineage!

Equally, sponges are just as old as non-sponge animals, so calling them “old” is a tad dodgy. Here, you could argue that sponges have been around longer than, say, vertebrates, which is true to the best of our knowledge. In that sense, “sponges” is an older lineage than “vertebrates”. But that only means that “sponges” should be compared to “non-sponges” rather than “vertebrates”, and anyone making such comparisons should be as aware of the diversity lurking within sponges as they are of the diversity of other animals.

The “evolutionary old animals” quote actually comes from a paper that looked at stem cell genes in Hydra to understand the evolution of stem cells in animals. (Hemmrich et al., 2012). It’s not comparing cnidarians (the phylum hydras belong to) to something genuinely younger than them. I can’t resist quoting the whole offending sentenc:

Our observations provided new and comprehensive insight into the complex network that orchestrates patterning and tissue homeostasis in an evolutionary old animal that branched off almost 600 million years ago. (p3277)

Honestly, what does that even mean? Branched off from what?

OK, I know it means from our own ancestors. But my point is that this should not be taken for granted, and if you do take a human-centric point of view, you should bloody well make that explicit. You should not write as though evolution had some sort of “main branch” leading to us from which things split every now and then. Lineages split from each other.

You might think that I’m being pedantic just to have an excuse to rant, but the implicit views underlying examples like the above have real consequences for the study of evolution. Namely, they might lead scientists to assume that representatives of “basal” lineages got stuck in the Precambrian and could just stand in for their distant ancestors. This is dangerous.

Take sponges. Yes, in many respects they probably resemble the first animals more than we do. Chances are those ancient animals didn’t have sophisticated organs and like two hundred different cell types. However, chances also are that they were made of distinct cells rather than huge merged syncytia, and that they didn’t have elaborate skeletons made of some sort of mineral, both of which are properties of many sponges. All animals alive today had exactly the same amount of time to evolve their own quirks since their last common ancestor. We shouldn’t just assume that anything “simple” in an animal we regard as “basal” is inherited straight from that ancestor just because it fits our favourite story.

Case in point: the Amphimedon genome was found to be impoverished in many families of developmentally important “master” genes, and this fit nicely into the prevailing view of the increasing complexity of animals throughout their history (Larroux et al., 2008). But it’s likely that at least some of those genes were actually lost by Amphimedon‘s ancestors and not gained by ours (Mendivil Ramos et al., 2012). Assuming that “basal” (relative to us) means “similar to ancestor X” can very easily lead to unwarranted conclusions, and that can hinder our ability to figure out what really happened. To me, that’s a big deal.

***

References:

Hemmrich G et al. (2012) Molecular signatures of the three stem cell lineages in Hydra and the emergence of stem cell function at the base of multicellularity. Molecular Biology and Evolution 29:3267-3280

Larroux C et al. (2008) Genesis and expansion of metazoan transcription factor gene classes. Molecular Biology and Evolution 25:980-996

Mendivil Ramos O et al. (2012) Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals. Current Biology 22:1951-1956

Sperling EA et al. (2010) Where’s the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing  Precambrian fossil record of siliceous sponge spicules. Geobiology 8:24-36

Srivastava M et al. (2008) The Trichoplax genome and the nature of placozoans. Nature 454:955-960

Pictures, thousand words, and a shout-out to UC Berkeley

One of my pet peeves – probably my biggest pet peeve – about depictions of evolution is how everything is always focused on its “pinnacles” (read: us).

I have a lovely t-shirt from BioMed Central, publisher of awesome open-access science journals. It has a nicely designed tree of life on the front, wrapped up in a stylised cell membrane. I think that’s a really neat idea, and graphically, it’s executed in a very attractive way.

I really don’t like the contents of the tree.

Look at the organisms with the little silhouettes. There are 30 figures, 12 of which are vertebrates, 5 of which are mammals. Arthropods, the most species-rich animal phylum by a margin bigger than the rest of the animal kingdom, are dwarfed in comparison. A single clutch of assorted prokaryotes stands in for two of the three great domains of life, and single-celled eukaryotes are absent except for some yeasts. The tree isn’t even fair to vertebrates. Mammals (5 figures) number between 5-6000 known species, birds (1 figure) around 10 000, ray-finned fishes (1 figure) well over 20 000.

Maybe I wouldn’t mind this sort of thing so much if it didn’t reinforce most people’s unconscious (and completely wrong) picture of evolution. But as the wise man said, pictures are worth a thousand words, and this picture screams that everything aside from mammals is the “miscellany” of biodiversity. (I guess they did treat plants pretty fairly. I’ll give them that.)

This is why I was madly happy to find this:

The picture is from UC Berkeley’s Understanding Evolution site, which I already loved to pieces, but spotting this gem made me love it even more. This is how a tree of life should be illustrated. Clear, pretty, colourful, decorated with nice pictures – and completely non-mammal-centric. Since you are an animal and presumably interested in your own kind, you can click to zoom in on animals, then on vertebrates (which doesn’t actually work for me), but first you are confronted with the tininess of our corner of the tree. I especially love how they didn’t pick a vertebrate (let alone a mammal) to represent animals among the photos.

I’m probably being unfair here, comparing a t-shirt design made purely for aesthetic reasons and a diagram fully intended to educate. Still, a tree of life divided this way can be just as pleasing to the eye as a tree of life pretending that mammals are the point of evolution – and it’s not even the case that BMC Biology, which the t-shirt advertises, is a mammal-specific journal. I think it wouldn’t hurt for t-shirt designers to re-examine their default settings every now and then 🙂

“That innocent little word ‘to'”

It seems the editor-in-chief of the review journal BioEssays shares my concerns about using teleological language when discussing evolution. He calls it anthropomorphic rather than teleological, which is probably a better way of putting it – likely, the reason we think of evolution in teleological terms in the first place is because we do things for purposes, and we are biased to think of everything as if it had a human mind. The word “anthropomorphism”, I think, gets to the root of the problem.

In his short opinion piece “We need a new language for evolution… everywhere” (BioEssays 33:237), Andrew Moore discusses how language (including “that innocent little word”) can subtly lure scientist and layperson alike into this dangerous trap.

I especially like this bit:

Another concept that arises from the ‘anthropomorphisation’ of evolution is the ‘problem’: in other words, an organism or system evolves towards what we, retrospectively, identify as a barrier, or ‘problem’ that had to be ‘solved’, and we wonder how it was overcome. Nature doesn’t solve anything.

(It’s a point I’ve never quite articulated to myself, so these remarks were something of a lightbulb moment for me.)

Moore doesn’t just tear down the old language. He provides a table listing some common turns of phrase that give entirely the wrong impression – and offers alternatives that, for the most part, aren’t clumsy at all. (I’ve got to say, though, that calling the alternatives “new-speak” is a tad ironic in an article about using the wrong language, IMO.) Interestingly, one of his “replacements” still sounds teleological/anthropomorphic to me. Instead of “innovation of evolution”, he suggests using “product”, and my first thought upon hearing that word tends to involve factories. Just goes to show how difficult it is to get rid of deeply ingrained thought patterns.

Still, kudos to Moore. For bringing the problem to the fore, and for suggesting specific ways of solving it.

The folly of hindsight

Recently, I’ve been re-reading Life on a Young Planet. As I said before, it’s an excellent book. It is beautifully written, cleverly structured, and the author is obviously knowledgeable about the subject (which, sadly, isn’t always true in popular science). Most importantly, it emphasises the process of science, as opposed to the actual knowledge gained through that process. “How do we know what we know?” is a question at least as important to Andrew Knoll as “What do we know?” As he so eloquently puts it, “[t]extbooks may portray science as a codification of facts, but it is really a disciplined way of asking about the unknown.” This is an attitude I share with him, and probably a big part of the reason the book has such a special place in my heart.

So, I was surprised to discover on this re-read that Knoll falls into one of the most common traps of talking about evolution: teleological thinking. In Chapter 11, “Cambrian Redux”, he writes that “[f]orty million years after the Cambrian began, evolutionary way stations still played a major role in the ecology of marine environments.” He is discussing the Cambrian explosion, of course, and here he is talking about stem groups of living phyla living alongside the crown groups [1]. I don’t think he means to convey a sense of goal-orientation, but the wording does exactly that. It sounds as if, say, Anomalocaris was just something evolution had to pass through to get to arthropods, not a successful animal in its own right. It suggests that the eventual supplanting of these now-extinct lineages was meant to happen.

Richard Dawkins called this “the conceit of hindsight” and complained about it at length in the introduction to his (also really good) book The Ancestor’s Tale. Dawkins characterises such thinking as “seeing the past as aimed at our own time, as though the characters in history’s play had nothing better to do with their time than foreshadow us.” (In this particular case, he’s talking about ordinary history, as a prelude to introducing the same problem in evolutionary history.) It’s a very common way of thinking about evolution (just look at any of the traditionalmarch of progressimages), and it’s also totally wrong.

If you’ve been in prolonged contact with creationists, you’ve almost certainly encountered conspicuous examples of this common misconception. Types of questions I’ve personally seen include “what use is half a wing/[insert transitional feature here]?”, “why didn’t all X evolve into Y?”, and “how did X know they were evolving into Y?” At the heart of each lurks the idea that evolution works towards goals. That it doesn’t seems to be one of the most difficult aspects of evolutionary theory to grasp, and it’s especially hard to escape when we are looking at the past.

Simply put, evolution has no foresight. Rather than working towards something, the process always reacts to something. Rather than looking ahead, it constantly lives in the present, though it’s often saddled with the baggage of the past. The kinds of things that cause mutation (such as replication errors, radiation and chemical damage) have random effects [2]. Moreover, the processes that sort among mutations, such as natural selection, are similarly blind. Because the mechanisms of evolution are not thinking entities, the only traits that get passed on are traits that help their owners reproduce in the here and now. Any long-term trend is the outcome of repeated rounds of selection on the same traits. Evolution has no goal in the same way a snowflake doesn’t aim for your nose, though in retrospect you can perhaps reconstruct the path it took to get there.

That’s the problem with history: we are looking back on processes whose outcomes we already know. It’s so tempting to view the preceding events as mere stages in a journey aimed at those outcomes. After all, we humans work with goals in mind all the time (ironically, nowadays we might use evolutionary principles to attain those goals!). Unfortunately, viewing evolution in this way can lose sight of the process by focusing on the endpoint – and then people start asking about half wings.

It’s important to remember that the ancestor of the wing was not “half a wing”. It was just a modified arm that had some advantage over its ancestor, e.g. large feathers to help a dinosaur keep her eggs warm, or (closer to “wingness”) glide from tree to tree. These animals weren’t half-functional fliers, they were fully functional at whatever they were doing. If an alien scientist looked around in a Middle Jurassic forest, it might have marvelled at the exquisite gliding adaptations of small dinosaurs much like Microraptor [3], but it surely wouldn’t have focused on how bad they were at flying.

(Also, always remember that when you are the only one who can do something, by definition you’re the best at it!)

I wish we could just drop the teleological language altogether. It’s surprisingly difficult even when you actively try, though. It could be something about the way language works (at least the two I know well). Somehow, it seems much easier to say things like “X evolved to do Y” in them than to give a more accurate description of the evolutionary process. I’m sure that says something profound about human minds…

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[1] In systematic jargon, a crown group is the last common ancestor of all living members of a group, and all of its descendants (including extinct ones). The corresponding stem group (stem groups are always relative to a crown) includes anything extinct that’s more closely related to the crown group in question than to any other living lineage. For example, all non-avian dinosaurs were stem birds.

[2] We have to be precise about the meaning of “random” here. Some mutagens cause very specific mutations. “Random” refers to their fitness effects, not the chemical changes that happen or even the places where they happen (though the latter is largely random, except for trivial constraints). The same mutation in different parts of the genome can be beneficial, harmful or have no effect at all, and conversely, the same is true for different mutations at the same spot – and all of this is uncontrollable. If you keep your study organisms in a hot environment, they won’t suddenly start producing more mutations that make them heat-resistant. That’s the main thing we mean when we say mutations are random.

[3] Microraptor itself is Early Cretaceous – birds were already around when these guys inhabited the forests of China. The first part of the Jurassic – i.e. the time between early dinosaurs and Archaeopteryx – doesn’t have a great record of dinosaur fossils, so most of what we know of the origin of birds comes from relatives of birds that persisted alongside birds later on. However, a few very bird-like fossils are contemporaneous with, or older than, Archaeopteryx. Like Microraptor, some of these creatures have long leg feathers (unlike Microraptor‘s, theirs aren’t very aerodynamic) , so that may be something ancestral for the “birdy” lineage.