I’m starting to like this Andrew Moore guy

He’s the editor-in-chief of BioEssays, a journal dedicated to publishing reviews and “ideas papers” in biology. Last year, I was very happy about his editorial concerning anthropomorphic language in evolutionary biology. Now he’s written another one that makes me want to hug him. It’s about recognising scientists who don’t produce bucketloads of data.

He argues that both in education and funding, there is far too much emphasis on data generation, and far too little on data integration, that is, taking others’ results and making some sort of overarching sense of them. He writes:

The problem starts early: as undergraduates, students learn the foundations of the subject; they then passage to learning how to do research – the emphasis being on generating results. Why the overwhelming preoccupation with generating more results? Aren’t there enough being produced? Arguably there are so many results around that we need more dedicated people who explicitly don’t produce new results, but rather distill out higher level insights. Naturals at this kind of science can also be spotted in the lab: supervisors should be mindful not to automatically denigrate diffuse interest or lack of single-mindedness: perhaps they are the signs of an “integrator”. And an “integrator” is every bit as much a scientist as a “producer”.

As a person for whom generating results is usually a chore while thinking about them is a joy, all I can say is: WORD.

Of really old maybe-sponges, molecular clocks and common ancestors

If you’ve ever visited this blog before, you probably know that the early evolution of animals is one of my many random interests. You could say it’s my main interest, though that may be less obvious from my posting record so far. Well, knowing that, you could imagine my face when my labmate pointed me to this National Geographic news piece.

It doesn’t surprise me much that the earliest known animal would be like a sponge. Although for what they do, their construction is nothing short of ingenious, sponges are comparatively simple animals. While it’s possible that they weren’t always like that, it appears that their genomes are devoid of lots of the genes other animals have added to the “toolkit” that fashions their complex bodies (Larroux et al., 2008). They also retain morphological features that were probably present in the ancestors of animals and lost in pretty much every other animal lineage alive today. Notably, their food-capturing cells look an awful lot like the cells of choanoflagellates, which are thought to be the closest living relatives of animals and perhaps similar in appearance to our distant ancestors.

What looks positively amazing about the newly described sponge-like thingies, who go by the deceptively Italian-sounding name of Otavia (they’re actually named after the Otavi Group of rock formations in Namibia), is their age. The oldest ones, apparently, are close to 760 million years old, perhaps 180 million years older than the earliest occurrences of the famous and mysterious Ediacaran animals (Narbonne, 2005). (By the way, that difference is about the length of the “age of dinosaurs”!) The news, and Brain et al. (2012), point out that this date also precedes some events that were thought to set the stage for the rise of animals: the giant ice ages known as Snowball Earths, and the rise in atmospheric oxygen levels towards the end of Precambrian times.

We could talk about the significance of that, I suppose, but the issue the whole discovery brought to my mind is, strangely, molecular clocks.

Let’s face it, the Precambrian fossil record of animals is not brilliant. It’s getting better, as more Ediacaran fossils are dug up and analysed with more sophisticated methods, but it still raises as many questions as it answers, and the earliest history of animals is still shrouded in mystery. For one thing, when did animals even evolve? All we know from fossils is that it must have been “before”. If a particular fossil is not only an animal, but member of an identifiable subgroup of animals, it means that the branch separating that subgroup from all other animal lineages must have split by that time. A number of Precambrian animals may be members of groups that are many such splits into the animal family tree, and things that look like the predecessors of those splits are difficult to identify in the fossil record. So where did they come from? Where did it all begin? Kind of hard to say based on the bunch of hard to interpret blobs, fronds and strange fractal bodies that is the Ediacaran biota.

When the fossil record speaks gibberish, people sometimes query another keeper of deep evolutionary history: DNA. Molecular clock methods date splits between lineages by counting differences between their living members. The basic idea is this: if most mutations have no effect on fitness, then most mutations are created equal, with the same chance of fixing themselves in the gene pool. If that is true, then genomes change at roughly constant rates – dependent only on mutation rate – over time. Using that assumption and lineages whose divergence time is known (usually, from good fossil records), you can translate the genetic differences between two or more groups into evolutionary time.

The problem is that real life is not so simple as that. Evolution is not always neutral. The same gene may behave like a clock in one lineage or during one time period and not another. Part of a gene may be a good clock while another part isn’t. Even if all of a gene evolves in a clock-like manner in all lineages under study, there’s no guarantee that the clock will tick at the same rate in all of them. Different genes or parts of a gene can tick at different rates, and this can vary over time. If we’re trying to measure very long times, it can be hard to correctly estimate the amount of change in a gene. There can be error in the fossils used for calibration, or the calibrating lineages may evolve differently from the ones we’re interested in. And so on.

And thus, published estimates for early divergences among animals range from numbers that make reasonable sense with the fossil record (e.g. Peterson et al., 2004), to some that throw another billion years on top of those numbers (see Chapter 11 in Knoll [2003] for an accessible discussion).

The problem, as I see it, is this. With a billion-year margin of error, some of those estimates must be wrong. As Andrew Knoll noted, they all require that animals began much earlier than their fossil record (at least as it was known at the time). How can we trust any of them? Even for the ones that match what we think of the fossil record – well, stopped clocks are accurate twice a day. For a scientist, being accidentally right is no better than being wrong.

I suppose Otavia, if it’s really a sponge-ish creature, fits the Peterson & co. estimates quite neatly. Fairly certain bilaterians like Kimberella are known from the White Sea assemblage of the Ediacaran, somewhat under 560 million years ago (Narbonne, 2005). The origin of bilaterians is somewhere between two and four splits[1] after sponges diverged from other animals. Peterson and colleagues estimated it between 573 and 656 million years ago – so if sponges are indeed a conservative bunch, sponge-like animals must have been around quite a bit earlier, but perhaps >1 billion years ago is really stretching it. 760 million sounds kind of nice, farther back than the Kimberellas and Dickinsonias but not too far.

Kind of. But, seeing as we’ve had to wait this long for a maybe-sponge that old, who’s to say even older animals aren’t hiding in some unexplored fossil bed? Who’s to say that the next “oldest animal” find won’t validate some of the more outlandish estimates?

The other thing I’m wondering about re: Otavia is: is it a sponge (assuming it’s an animal at all), or could it belong to a lineage ancestral to both sponges and other animals? (Were early sponges ancestral to other animals? The idea has been played with in phylogenetic circles…) I guess we’ll never know for certain. I still think it’s worth raising the question. Creatures that might be ancestral to more than one phylum are extremely valuable to evolutionary biologists, but they might be very hard to recognise for what they are. Part of the problem with Ediacaran animals is that many if not most of them lack features associated with living phyla – but that’s exactly what we would expect from creatures that preceded the divergence of those phyla! Given how little, say, a jellyfish and a snail have in common, what on earth would their common ancestors look like? Would they have any fossilisable characteristics at all that could give us a hint as to their family ties?

And I guess I’ll close today’s musings with that question. If I spent more time reading Brain et al. (2012), there’d probably be a lot more to discuss, but after doing lab work all day and spending an extra couple of hours writing this, my brain doesn’t feel up to it 🙂


[1] You can refer to the rough animal phylogeny in the Nectocaris post for the moment. Being slightly out of the loop in this area, I wouldn’t hazard a guess as to the relationships of ctenophores, cnidarians and placozoans, hence my uncertainty. It’s possible that these three all form a single branch with bilaterians on the other side. Or they could represent three different branching events, or anything in between. I really should make an animal phylogeny page, I think, since I keep finding myself wanting to talk about bilaterians and lophotrochozoans and things that don’t make much sense unless you know at least the basics shown in tree I made for Nectocaris



Brain CK et al. (2012) The first animals: ca. 760-million-year-old sponge-like fossils from Namibia. South African Journal of Science 108:658; doi:10.4102/sajs.v108i1/2.658

Knoll AH (2003) Life on a Young Planet. Princeton University Press.

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

Narbonne GM (2005) The Ediacara biota: Neoproterozoic origin of animals and their ecosystems. Annual Review of Earth and Planetary Sciences 33:421-442

Peterson KJ et al. (2004) Estimating metazoan divergence times with a molecular clock. PNAS 101:6536-6541