Fifty thousand generations, still improving

I take all my hats off to Richard Lenski and his team. If you’ve never heard of them, they are the group that has been running an evolution experiment with E. coli bacteria non-stop for the last 25 years. That’s over 50 000 generations of the little creatures; in human generations, that translates to ~1.5 million years. This experiment has to be one of the most amazing things that ever happened in evolutionary biology.

(Below: photograph of flasks containing the twelve experimental populations on 25 June 2008. The flask labelled A-3 is cloudier than the others: this is a very special population. Photo by Brian Baer and Neerja Hajela, via Wikimedia Commons.)

It doesn’t necessarily take many generations to see some mind-blowing things in evolution. An irreducibly complex new protein interaction (Meyer et al., 2012), the beginnings of new species and a simple form of multicellularity (Boraas et al., 1998) are only a few examples. However, a few generations only show tiny snapshots of the evolutionary process. Letting a population evolve for thousands of generations allows you to directly witness processes that you’d normally have to glean from the fossil record or from studies of their end products.

Fifty thousand generations, for example, can tell you that they aren’t nearly enough time to reach the limit of adaptation. The newest fruit of the Long-Term Evolution Experiment is a short paper examining the improvement in fitness the bacteria experienced over its 25 years (Wiser et al., 2013). “Fitness” is measured here as growth rate relative to the ancestral strain; the faster the bacteria are able to grow in the environment of the LTEE (which has a limited amount of glucose, E. coli‘s favourite food), the fitter they are. The LTEE follows twelve populations, all from the same ancestor, evolving in parallel, so it can also determine whether something that happens to one population is a chance occurrence or a general feature of evolution.

You can draw up a plot of fitness over time for one or more populations, and then fit mathematical models to this plot. Earlier in the experiment, the group found that a simple model in which adaptation slows down over time and eventually grinds to a halt fits the data well. However, that isn’t the only promising model. Another one predicts that adaptation only slows, never stops. Now, the experiment has been running long enough to distinguish between the two, and the second one wins hands down. Thus far, even though they’ve had plenty of time to adapt to their unchanging environment, the Lenski group’s E. coli just keep getting better at living there.

Although the simple mathematical function that describes the behaviour of these populations doesn’t really explain what’s happening behind the scenes, the team was also able to reproduce the same behaviour by building a model from known evolutionary phenomena. For example, they incorporated the idea that two bacteria with two different beneficial mutations in the same bottle are going to compete and slow down overall adaptation. (This is a problem of asexual organisms. If the creatures were, say, animals, they might have sex and spread both mutations at the same time.) So the original model doesn’t just describe the data well, it also follows from sensible theory. So did the observation that the populations which evolved higher mutation rates adapted faster.

Now, one of the first things you learn about interpreting models is that extrapolating beyond your data is dangerous. Trends can’t go on forever. In this case, you’d eventually end up with bacteria that reproduced infinitely fast, which is clearly ridiculous. However, Wiser et al. suggest that the point were their trend gets ridiculous is very, very far in the future. “The 50,000 generations studied here occurred in one scientist’s laboratory in ~21 years,” they remind us, then continue: “Now imagine that the experiment continues for 50,000 generations of scientists, each overseeing 50,000 bacterial generations, for 2.5 billion generations total.”

If the current trend continues unchanged, they estimate that the bugs at that faraway time point will be able to divide roughly every 23 minutes, compared to 55 minutes for the ancestral strain. That is still a totally realistic growth rate for a happy bacterium!

I know none of us will live to see it, but I really want to know what would happen to these little guys in 2.5 billion generations…



Boraas ME et al. (1998) Phagotrophy by a flagellate selects for colonial prey: a possible origin of multicellularity. Evolutionary Ecology 12:153-164

Meyer JR et al. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335:428-432

Wiser MJ et al. (2013) Long-term dynamics of adaptation in asexual populations. Science, published online 14/11/2013, doi: 10.1126/science.1243357

In which fangirling turns into philosophy

Textbooks may portray science as a codification of facts, but it is really a disciplined way of asking about the unknown. — Andrew Knoll, Life on a Young Planet

Some books change your life. When I was 12 or 13 or thereabouts, SJ Gould and others’ Book of Life rekindled my interest in prehistoric life, introduced me to the Cambrian explosion, and opened my eyes to a whole new worldview. It’s one of the reasons I hold a degree in evolutionary biology.

Life on a Young Planet was not a life-changer, precisely. That’s not why I love it to pieces. By the time I read it, I’d gained an appreciation of just how complex and full of uncertainty natural science was, and the book was permeated by an awareness of this complexity. Also, it was simply beautiful writing.

(I can’t emphasise the importance of good writing enough. I’ve read too many papers and books [Crucible of Creation and The Plausibility of Life, I’m looking at you] that had good information but were so atrociously written that I nearly put them down despite being fascinated by their subject.)

Last month, the author of Life on a Young Planet, Harvard professor Andy Knoll, came to visit my university. I was practically bouncing with excitement from the moment I saw his name on a newsletter. He gave four lectures in total; until the very last one, I actually contemplated getting my copy of the book signed. Or, to be a fangirl and a nerd, my printout of his lovely biomineralisation review. (I still can’t decide if I made a mistake. Damn, I didn’t even ask a stupid question. Four lectures, and I just sat there and drooled over my notebook.)

Knoll is nearly as good a speaker as he is a writer. He doesn’t have the liveliest voice and speaks quite slowly, but if you can get past that, his lectures are really good. (I’m glad of that; I really don’t like losing my illusions!) They are solid structures that you have no difficulty following the logic of.

Let me put it this way – Andy Knoll is an excellent storyteller.

That got me worrying, because I’m a sceptic and (truth be told) a little bit of a cynic at heart, and because over the years I’ve done a lot of navel-gazing about belief and knowledge and conviction. I have a tendency to grow suspicious when I feel too certain about something.

Am I – are we – too often blinded by good storytelling? How often do we get so enamoured of good ideas that we try to force them on situations they don’t fit? And how often do we doubt something just because it sounds too neat?

Here’s the specific example from the Knoll lectures that made me think of this. Knoll is a champion of the oxygen + predation explanation of the Cambrian explosion. (I didn’t realise he was involved in that paper until it came up in the lectures…) He is also an advocate of a similar explanation for the diversification of single-celled eukaryotes 250 million years before the Cambrian. He convinced me well enough, but then I immediately thought – really? Is it really that simple? Does one size really fit both events?

I often take note of these “pet ideas” as I read scientific literature. A group of phylogeneticists uses microRNAs to tackle every tough problem ever. A palaeontologist interprets every squishy-looking Cambrian weirdo as a mollusc. Researchers in the biomineral field look for slushy amorphous precursors to crystalline hard parts everywhere. (Remember, all generalisations are false ;))

Just to be clear: I’m not at all saying that being a “pet idea” automatically makes something wrong or suspicious. For instance, the hunters of amorphous biominerals have some good theoretical reasons to look, and they often do find what they’re looking for. Likewise, I’m impressed enough with Andy Knoll’s pet hypothesis about the Cambrian that I’ve rethought my own pet ideas about the subject.

I’m also not accusing these people of being closed-minded. Going back to Knoll, IMO he demonstrated ample healthy scepticism about his pets during his post-lecture Q&A sessions. (Which makes me a bit less nervous about the neatness of his stories.)

Someone better versed in the philosophy and sociology of science could probably write a long treatise involving paradigms and confirmation bias and contrariness here. I’m even less of a philosopher than I am a geologist, so I think I’ll leave the deeper insights to those who have them.

Meanwhile, I’ll continue to be a fan of Andy Knoll and appreciate a good scientific story. So long as I remember to look beneath the surface – both of good stories and of my own suspicion of them…


Fanworm fandom

In all my meanderings so far, I have never talked about my work in more than vague references to my connection to biominerals. Well, today won’t be the day I really start, but I would like to introduce the animals I work with. Because they are beautiful, awesome, and I love them (except when they’re sabotaging my experiments :-P). They are fan worms.

“Fan worm” is a bit of a loose term, and I’m still not entirely sure what group of worms it is/isn’t supposed to apply to. The group of fan worms I’d like to talk about today is family Serpulidae. (Call them “serps”. They won’t mind.)

Serpulidae are, if the latest phylogenetic research is to be believed, a subgroup of another “family”, the Sabellidae or feather duster worms (Kupriyanova and Rouse, 2008). All sabellids are sedentary filter-feeders. They live in tubes, putting a feathery crown of tentacles out into the water to catch their microscopic food. This is the fan in fan worm, and it’s all that most people ever see of these gorgeous creatures. It’s also today’s excuse to post some Nick Hobgood Christmas tree worms from Wikipedia, although their crazy spiralling tentacle crowns are not all that fan-like. (Bottle brush worms? :D)

These guys in the photo are mostly buried in a coral colony, with only their tentacle crowns sticking out.

Ancestrally, sabellid tubes are made of hard particles like sand and shell fragments glued together with mucus secreted by the worm. Serpulids are special in that they make their own hard material – calcium carbonate – instead of picking stuff up from the environment.

Serpulid tubes can have a highly organised structure that betrays sophisticated tube-building mechanisms (Vinn et al., 2008). Incidentally, some of them are pretty awesome if you look close enough. Below are the rather bland-looking tubes of Ditrupa arietina lying on the seafloor (from ten Hove and Kupriyanova [2009]). Then an electron microscope image of the outer tube layer showing the cool jigsaw-like cross sections of the calcareous rods it’s made of (Olev Vinn via Wiki Commons).


The general anatomy of the animal inside the tube is demonstrated quite nicely in the photograph below, from ten Hove and Kupriyanova (2009):


This is Serpula vermicularis, the species that gave its name to the family. The head end, obviously, is the one with the tentacles. Below it is a rather elegant thorax wearing a jacket of skin flaps (technically, “thoracic membranes”), with a wide collar folding down over the top. The collar builds the tube: when the worm wants to expand its home, it pokes its head out, wraps its collar over the rim, and deposits a new layer of material from glands under the collar.

The weird funnel-shaped thingy sticking out Serpula‘s head above is called an operculum. It’s another speciality of (most) serpulids, functioning in defence against predators. It’s used to close off the tube, but – at least in my species – it’s also a sacrifice body part that pops off at a predetermined point if you tug or prod it too hard. A bit like a lizard’s tail. (Or a sea cucumber’s guts, because gross examples are always better.) Also like the lizard’s tail, the operculum regrows easily, but unlike lizards, serps can regenerate a perfect new operculum. Some serps, including mine, have upgraded their defences further by reinforcing the operculum with calcium carbonate. A calcified body part that you can make develop on demand. What more can you dream of? 😉

Serpulids are found all over the world. Most of the 300+ species live in the sea, all the way from tidal rock pools to deep sea vents. There are a few that can handle brackish water, and there’s a single species that somehow found its way into freshwater-filled limestone caves along the Adriatic coast. According to Kupriyanova et al. (2009), this little explorer is closely related to the brackish-water species, so serps probably only figured out how to deal with lower salinity once.

They are nowhere near as famous as corals, but a few serpulid species are prolific reef builders. Ficopomatus enigmaticus (one of the brackish serps) can grow in roundish reefs made of generations of worm tubes. Although the individual tubes are only a few cm long, reefs can reach several metres across.

F. enigmaticus is an invasive species. Hitchhiking from their European homeland on boats and spawning wherever they felt happy enough, the worms have spread across the warm, shallow, brackish waters of the world. Below, their reefs are shown polka dotting the Mar Chiquita lagoon over in Argentina (photos: Alejandro Bortolus, in Schwindt et al. [2001]). Note the scale bar!


F. enigmaticus reefs have a pretty big ecological impact in their new territory. Their filter-feeding makes the water less murky (Bruschetti et al., 2008), which is good for the seafloor community, not so great for the phytoplankton that caused the murkiness. The reefs provide hiding places for native predators, changing the composition of the seafloor community (Schwindt et al., 2001), and they can also serve as resting stops and hunting grounds for birds (Bruschetti et al., 2009).

And finally, let’s talk a bit about serpulid babies, because baby worms are the best. I don’t know about other serps, but my species has very stylish BABY PINK EGGS. The moment you remove an adult worm from its tube, it panic-spawns all over the place. If you mix the pink eggs with the boring white sperm in some seawater, by the next day the dish will be full of tiny, zipping white balls. (At this point you’d better feed them, since unlike some other baby polychaetes, they don’t get a lot of food from mum. In nature, they’d swim off and live in the plankton, hunting tiny algae until they are ready to settle.)

In another day or two, the little balls grow quite a bit and turn into textbook examples of the type of larva known as the trochophore. If you’re good to them and give them enough food, they’ll keep growing like crazy. You can always see whether they’re hungry or not, since they are transparent and the colourful algae they like to eat show through their skin. This one, from McDougall et al. (2006) via Wiki Commons, was clearly well-fed when it fell victim to science:

They look all hairy around the broadest part – those are the cilia they use to swim. They are very good at swimming! Within a couple of weeks, they’ve transformed into a more mature form with three newfangled segments and a lovely pair of eyes, like this other one from the same paper:

They are now sniffing along the bottom, looking for a place to settle. When they find a spot they like, they lie down, secrete a tiny tube (made of just mucus at first), and metamorphose into transparent baby worms complete with an operculum and everything. This is what Pomatoceros lamarckii looks like mid-metamorphosis (again from McDougall et al.):


At this point, they are a bit ugly, but don’t worry, the ugly wormling stage doesn’t last long. I’ll finish off with one of my own photos what they turn into:


These are slightly over three weeks old, and they have tiny, iridescent tentacles and minute, transparent opercula. Their now-calcified baby tubes are just a few mm long.

Aren’t they lovely? 😀



Bruschetti M et al. (2008) Grazing effect of the invasive reef-forming polychaete Ficopomatus enigmaticus (Fauvel) on phytoplankton biomass in a SW Atlantic coastal lagoon. Journal of Experimental Marine Biology and Ecology 354:212-219

Bruschetti M et al. (2009) An invasive intertidal reef-forming polychaete affect habitat use and feeding behavior of migratory and locals birds in a SW Atlantic coastal lagoon. Journal of Experimental Marine Biology and Ecology 375:76-83

Kupriyanova EK & Rouse GW (2008) Yet another example of paraphyly in Annelida: molecular evidence that Sabellidae contains Serpulidae. Molecular Phylogenetics and Evolution 46:1174-1181

Kupriyanova EK et al. (2009) Evolution of the unique freshwater cave-dwelling tube worm Marifugia cavatica (Annelida: Serpulidae). Systematics and Biodiversity 7:389-401

McDougall C et al. (2006) The development of the larval nervous system, musculature and ciliary bands of Pomatoceros lamarckii (Annelida): heterochrony in polychaetes. Frontiers in Zoology 3:16

Schwindt E et al. (2001) Invasion of a reef-builder polychaete: direct and indirect impacts on the native benthic community structure. Biological Invasions 3:137-149

ten Hove HA & Kupriyanova EK (2009) Taxonomy of Serpulidae (Annelida, Polychaeta): The state of affairs. Zootaxa 2036:1-126

Vinn O et al. (2008) Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida). Zoological Journal of the Linnean Society 154:633-650


… sorry, guys. I did say something about squee and headdesk moments on my about page. ^_^;

It’s nothing big, really. I just got my hands on a book I’ve had on my wishlist for years, read a couple of chapters, and so far all I keep thinking is “neeeeeat!”

Dear editors and contributors, you all are officially making me happy. So happy that only the yay turtle can properly express my feelings!

(Seriously, who came up with this picture? It’s just perfect.)

We’ll read the rest of the book, and then we’ll see if Embryos in Deep Time is also as awesome as it sounds…

Another man after my own heart

It’s not terribly hard to turn me into a squealing fangirl. One of the ways is to agree with me eloquently and/or share my pet peeves. Another is to give me lightbulb moments. A third is to disagree with me in a well-reasoned, intelligent way. And finally, if I see you thoughtfully examining your own thinking, you are awesome by definition. Michaël Manuel’s monster review of body symmetry and polarity in animals (Manuel, 2009) did all of the above.

(In case you wondered, that means a long, squeeful meandering >.>)

Manuel writes about the evolution of two fundamental properties of animal body plans [1]: symmetry and polarity. You probably have a good intuitive understanding of symmetry, but here’s a definition anyway. An object is symmetrical if you can perform some transformation (rotation, reflection, shifting etc.) on it and get the same shape. Polarity is a different but equally simple concept – it basically means that one end of an object is different from the other, like the head and tail of a cat or the inner and outer arcs of a rainbow.

I can’t say that I’d thought an awful lot about either before I came across this review, so it’s not really surprising that I had lightbulbs going off in my head left and right while I was reading it. Because I didn’t think deeply about symmetry and polarity and complexity, I basically held the mainstream view I – and, I suspect, most of the mainstream – mostly picked up by osmosis.

That meant I fell victim to my own biggest pet peeve big time – I believed, without good reason and without even realising, that the body plan symmetries of major lineages of living animals represented successive increases in complexity. Sponges are kind of asymmetrical, cnidarians and ctenophores are radially symmetrical, and bilaterians such as ourselves have (more or less) mirror image symmetry, and these kinds of symmetry increase in complexity in this order. Only… they aren’t, and they don’t.

It turns out that this guy not only shares my pet peeve but uses it to demolish my long-held hidden assumptions. Double fangirl points!

Let there be light(bulbs)!

Problem number one with the traditional view – aside from ignoring that evolution ain’t a ladder – is that the distribution of symmetry types among animals is a little more complicated. Most importantly, most kinds of sponges are not asymmetrical. Most species may be, but that’s not the same thing. You see, most sponge species are demosponges, which make up only one of the four great divisions among sponges. Demosponges do have a tendency towards looking a bit amorphous, but the other three – calcareous sponges, glass sponges and homoscleromorphs – usually are some kind of symmetrical. All in all, the evidence points away from an asymmetrical animal ancestor. (Below: calcareous sponges being blatantly symmetrical, from Haeckel’s Kunstformen der Natur.)

The second problem is that my old view ignores at least one important kind of symmetry. Some “radially” symmetrical animals are actually closer to cylindrical symmetry. To understand the difference, imagine rotating a brick and a straight piece of pipe around their respective long axes. You can rotate the pipe as much or as little as you like, it’ll look exactly the same. In contrast, the only rotation that brings the brick back onto itself is turning it by 180° or multiples thereof. A pipe, with its infinitely many rotational symmetries, is cylindrically symmetrical, while the brick has a finite number of rotational symmetries [2], making it radially symmetrical.

Problem number three is that bilateral symmetry is actually no more complex than radial symmetry! What does “complexity” mean in this context? Manuel defines it as the number of coordinates required to specify any point in the animal’s body. In an animal with cylindrical symmetry, you only need a maximum of two: where along the main body axis and how far from the main body axis you are. Everything else is irrelevant, since these are the only axes along which the animal may be polarised. (Add any other polarity axis, and you’ve lost the cylindrical symmetry.)

Take a radially symmetrical creature, like a jellyfish. These also have a main rotational axis and an inside-outside axis of polarity. However, now the animal’s circumference is also divided up into regions, like slices in a cake. How does a skin cell around a baby jelly’s mouth know whether it’s to grow out into a tentacle or contribute to the space between tentacles? That is an extra instruction, an extra layer of complexity. We’re up to three. (Incidentally, here’s some jellyfish symmetry from Haeckel’s Kunstformen. [Here‘s photos of the real animal] A big cheat he may have been, but ol’ Ernst Haeckel certainly had an eye for beauty!)

And with that, jellies and their kin essentially catch up to the basic bilaterian plan. Because what do you need to specify a worm? You need a head-to-tail coordinate, you need a top-to-bottom one, and you need to say how far from the plane of symmetry you are. Still only three! Many bilaterians, including us, added a fourth coordinate by having different left and right sides, but that’s almost certainly not how we started when we split from the cnidarian lineage. (Below: radial symmetry doesn’t hold a monopoly on beauty! Three-striped flatworm [Pseudoceros tristriatus] by wildsingapore.)

Not only that, but Manuel argues that there’s very little evidence bilateral symmetry evolved from radial symmetry. By his reckoning, the most likely symmetry of the cnidarian-bilaterian common ancestor was cylindrical and not radial (more on this later, though). Thus the (mostly) radial cnidarians and the (mostly) bilateral bilaterians represent separate elaborations of a cylinder rather than stages in the same process.

There were a bunch more smaller lightbulb moments, but I’m already running long, so let’s get on to other things.

Respectful disagreement

I think my disagreements with Manuel’s review are more of degree than of kind. Our fundamental difference of opinion comes back to the symmetries of various ancestors and the evidence for them. He argues that key ancestors in animal phylogeny – that of cnidarians + bilaterians, that of cnidarians + bilaterians + ctenophores, and that of all animals – were cylindrical. (Below is the reference tree Manuel uses for his discussion, with symmetry types indicated by the little icons.)


I think he may well be correct in his conclusions, but I’m not entirely comfortable with his reasons. For example, he infers that the last common ancestor of cnidarians and ctenophores was cylindrical. One of his main arguments is that the repeated structures that “break up the cylinder” to confer radial symmetry are not the same in these two phyla. I think this is an intelligent point a smart guy who knows his zoology would make, so disagreement with it becomes debate as opposed to steamrolling [3].

Why I still disagree? As I said, it comes down to degrees and not kinds. Manuel considers the above evidence against a radially symmetrical common ancestor. I consider it lack of evidence for same. The situation reminds me of Erwin and Davidson (2002), which is also one of my favourite papers ever. They raise perhaps the most important point one could make about comparative developmental genetics: homologous pathways could have been present in common ancestors without the complex structures now generated by those pathways being there. Likewise, I think, radial symmetry could have been there in the common ancestor of cnidarians and ctenophores while none of the complex radially symmetrical structures (tentacles, stomach pouches, comb rows etc.) in the living animals were. Perhaps there were simpler divisions of cell types or whatnot that gave rise to the more overt radial symmetry of jellyfish, sea anemones and comb jellies.

In a related argument, Manuel discusses the homology (or lack thereof) of the dorsoventral axis in bilaterians and the so-called directive axis in sea anemones. Sea anemones actually show hints of bilateral symmetry, which prompted some authors (e.g. Baguñà et al., 2008) to argue that this bilateral symmetry and ours was inherited from a common ancestor (i.e. the cnidarian-bilaterian ancestor was bilateral).

I agree with Manuel that the developmental genetic evidence for this is equivocal at best. I even agree with him that developmental genetics isn’t decisive evidence for homology even if it matches better than it actually does in this case. But again, once the genetic evidence is dismissed as inconclusive, he relies on the non-homology of bilaterally symmetrical structures to conclude non-homology of bilateral symmetry. Again, I think this is a plausible but premature inference. Since I’m not sure whether homology or independent origin of bilateral symmetry is the better default hypothesis in this case, and I don’t think the evidence for/against either is convincing, I actually wouldn’t come down on either side as of yet.

But I can see his point, and that’s really cool.

Why else you’re awesome, Michaël Manuel…

Because you have a whole rant about “basal lineages”. I grinned like a maniac throughout your penultimate paragraph. Incidentally, you might have given me another favourite paper – anything with “basal baloney” in its title sounds like it’s worth a few squees of its own!

Because you apply critical thinking to your own thinking. See where we disagreed, non-homology of structures vs. symmetries, evidence against vs no evidence for, and all that? After you made the argument from non-homology of structures, I expected you to leave it at that. And you didn’t. You went and acknowledged its limitations, even though you stood by your original conclusions in the end.

Because you reminded me that radial symmetry is similar to metamerism/segmentation. I’d thought of that before, but it sort of went on holiday for a long time. Connections, yay!

Because you were suspicious about sponges’ lack of Hox/ParaHox genes. And how right you were!


Phew, that turned out rather longer and less coherent than I intended. And I didn’t even cover half of the stuff in my notes. I obviously really, really loved this paper…


[1] Or any body plan, really…

[2] Astute readers might have noticed that a brick has more than one axis of symmetry, plus several planes of symmetry as well. So it’s not only radially but also bilaterally symmetrical. The one thing it certainly isn’t is cylindrical 😉

[3] Not to say I don’t enjoy steamrolling obvious nonsense, but I also like growing intellectually, and steamrolling obvious nonsense rarely stretches the mind muscles…



Baguñà J et al. (2008) Back in time: a new systematic proposal for the Bilateria. Philosophical Transactions of the Royal Society B 363:1481-1491

Erwin DH & Davidson EH (2002) The last common bilaterian ancestor. Development 129:3021-3032

Manuel M (2009) Early evolution of symmetry and polarity in metazoan body plans. Comptes Rendus Biologies 332:184-209