The small joys in life

The other day I finally decided to get a good look at the underside of a chiton. I meet the little molluscs all the time; they live in the same rock pools my experimental animals come from. Usually, I just find them sitting on a rock being cryptic like these two I found on their Wikipedia page (photo: Hans Hillewaert):

They live in my head as these fascinating living fossils (even though if you ask me I’ll say that the whole concept of living fossils is stupid), strange beasties whose anatomy preserves relics of the time when molluscs were segmented animals. Now, I’m not sure molluscs ever actually were segmented animals, at least not to the same extent as, say, a centipede or a ragworm obviously is. (But “segmented” is a complicated property, and I don’t want to digress too far that way.)

Either way, I pried one of them off the stone I’d picked up and stuck it under the microscope, because biologists just can’t leave poor innocent creatures alone. I wanted to look for those signs of segmentation, which, by the way, are pretty much limited to the repetition of shell valves and gills unless you take the animal apart, in which case there are also muscles. I don’t know what I expected, really, but what I found was that the belly side of a chiton is mostly… boring.

(Unless it’s the size of this gumboot chiton, courtesy of Prof. Douglas Eernisse via Wikipedia. Then it’s pretty impressive and kind of scary.)

For one thing, most of it is covered by that fleshy foot that looks like a dog’s tongue that spent too much time in formalin. You are at the mercy of the chiton to even catch a glimpse of the gills, because the foot can very nicely spread out and cover them. And the gills themselves are sort of, well, anticlimactic. In fact, the entire underside of the poor chiton I abused (who, unlike the monster above, was barely the size of my pinkie nail) was just the same bland, wet shade of beige. At least Mr Gumboot above has brown gills.

It wasn’t a complete disappointment, though. For one thing, I’m oddly fascinated by that plump kissy mouth. It’s so… ugdorable. And then there is the girdle – the soft-tissue bit around the edges of the shell – which I totally didn’t know was covered in little projections. I was expecting something smooth and fleshy and maybe a bit slimy, like most things mollusc, and then bam, I zoomed in on it and it was all warty. In a pretty way. Wikipedia tells me that sometimes they have calcareous scales or spikes on the girdle. I didn’t prod my chiton enough to find out whether its warts were hard, but anything that involves biominerals is pretty interesting to me!

And don’t worry, the little chiton went back to its rock unharmed aside from the stress of getting turned on its back and prodded by a big scary creature. I’m not quite heartless enough to keep an animal I don’t need for my experiments. Even though I heart molluscs of all kinds* and I don’t care if their boring bellies disappointed me.

*Well, with the possible exception of the evil nudibranchs who also live in my rock pools and once ended up sliming all over my dish. Yuck.

Ocean Soda and the Animals

As far as scientific interests are concerned, I’m not an “environmental” person at all. Somehow, ecology and conservation managed to remain profoundly boring to me despite the fact that my heart breaks every time I think about the havoc we’re wreaking in the biosphere. The same is true for physiology except there’s not even much of an emotional response to that, aside from a sullen disgust accompanying memories of endless lectures about fish kidneys.

After telling you how much I don’t care about ecology and physiology, it probably doesn’t come as a surprise that this post is kind of about both. You see, I study an animal with calcareous hard parts. It just so happens that these days, animals like that may be in trouble. Humans are pumping insane amounts of carbon dioxide in the air at a (geologically speaking) stupid rate, the oceans are swallowing it and slowly turning into a very salty fizzy drink. Calcium carbonate and acid don’t get along.

As it happens, the subject of calcifying critters versus ocean acidification also fits one of my recurring themes, i.e. that things are usually more complicated than you think. In this case, things are certainly much more complicated than I suggested in the previous paragraph. And thus, you shall be treated to a meandering about some of the complications I’ve come across 🙂

Many, many sea creatures have hard parts – shells or skeletons – made of calcium carbonate, the mineral that also makes up limestone and marble. The long list includes stony corals, calcareous sponges, crustaceans, nearly all molluscs, starfish, sea urchins and other echinoderms, a few groups of segmented worms, and even such unlikely suspects as the “soft bodied” acorn worms (Cameron and Bishop, 2012). And then we didn’t even count the algae and assorted single-celled beasties that the food chains of these animals stand on. The bottom line is that calcium carbonate is a damn big ecological deal.

(Below: a selection of marine carbonate users from Nick Hobgood‘s Wikimedia stash. Because Nick Hobgood is amazing.)

Calcium carbonate (chemical formula CaCO3), of course, is made of calcium and carbonate ions. How easy it is for animals to put into a skeleton depends on a variety of factors. In the most trivial sense, it matters how much of the ingredients you give them. Calcium is a standard component of seawater everywhere. Carbonate is also found normally in seawater. Its abundance is in a dynamic equilibrium involving carbon dioxide, carbonate, bicarbonate, carbonic acid and water. I find the chemistry difficult to get my head around, so here’s a figure from Feely et al. (2001) for our collective education:

(The numbers are the concentrations of the various chemical species under pre-industrial atmospheric CO2 levels and doubled CO2 levels, which could easily happen in the not too distant future.)

As far as I understand this system, the problem with CO2 is twofold. First, adding more of it decreases the pH of the water, and all forms of calcium carbonate are much more soluble at lower pH. Second, it decreases the concentration of carbonate ions, which makes them harder to obtain for shell-making purposes. (The guy who wrote this Encyclopedia of Earth article probably understands the whole thing rather better than me, though.)

Because I’m a pedant, I have to note that ocean “acidification” is a bit misleadingly named, because normal seawater is (and will be for the foreseeable future) far from being actually acidic. But the rules still apply – the lower the pH, the more difficult it is to make solid CaCO3.

This seems like a straightforward equation – keep pumping CO2 into the air, and shellfish will soon be shell-less (and thoroughly screwed). However, when you look at the actual reactions of real living creatures to acidification treatments (which Kroeker et al., 2010 summarised the then-existing literature for) – or indeed what happens to said creatures in the wild (as this “historical” study of reef corals by Cooper et al., 2012 did), a slightly more nuanced picture emerges.

First of all, of course organisms aren’t passive and helpless players in this game. Just like we can sweat or shiver to keep our body temperature right, calcifying things can regulate the environment in which their skeletons are manufactured. A study that looked at the chemical environment of the specialised space in which corals build their skeletons found that the pH of the fluid there is always higher than that of the surrounding seawater – corals do their darnedest to keep it where it’s good for them (Venn et al., 2013).

Having a specialised, “insulated” space for mineral deposition is a pretty common thing in the living world. The tiny algae called coccolithophores (who are single-handedly responsible for the White Cliffs of Dover) simply make their characteristic plates (literally “limescales,” hehe) inside their cells. Echinoderm larvae merge cells to create a “spicule factory”. Molluscs deposit their shells into the protected space between a tough organic layer and the soft tissue of the mantle. Et cetera.

On top of that, all organisms have proteins specialised to transport ions through cell membranes. Creatures who build hard parts can use such proteins to actively shuttle the materials they need even when they’re working against physics.

Thus, most mineralising organisms have ways of dealing with environments not necessarily friendly to mineralisation. Some naturally have to handle a wide range of such environments, like shellfish who live in estuaries and experience changes in salinity (and calcium concentration, and pH) with every tide.

As you might expect, different organisms can react very differently to the same challenge, ocean acidification in this case (e.g. Ries et al., 2009). They could be badly affected, they could just not give a damn… or even up their game and increase their calcification rates, as a brittle star was observed to do (Wood et al., 2008). That sort of compensation appears costly in other areas, though – Wood et al’s brittle stars suffered muscle loss, for example. It’s also worth noting that even closely related species can be affected in pretty different ways. In a study of two oyster species of the same genus and similar natural habitats, the larvae of one just shrugged off a bit of acidification, whereas those of the other struggled to build their baby shells under identical conditions (Miller et al., 2009).

Overall, ocean acidification is going to be bad for most creatures who rely on calcified hard parts, but how bad and what kind of bad will vary greatly if the above examples are anything to go by.

However, carbon dioxide is not only known as an ingredient for sea soda. In fact, it’s probably better known as the baddie in the global warming story. The oceans aren’t just going to get lower on the pH scale. They are also getting warmer. And because scientists want to know everything, some of them went out and investigated what the combination of these two does to calcifying critters.

And there, in an ironic twist that allows us to feel a tiny bit of relief in the short term, they saw that a little warming (but not too much!) can actually mitigate the effects of acidification for some creatures. Make no mistake, baby sea urchins are still very screwed when you plunge them into “future” ocean water. But they are somewhat less screwed if you include warming in the package than if you just pump a load of CO2 into their tank (Byrne et al., 2010).

Calcifying animals in a real marine environment don’t exist in isolation – they prey on, are preyed on, help out and compete with members of other species. Will their different reactions to the changing chemistry of the ocean overhaul entire ecosystems? (I don’t read much ecological literature, so there are probably unseen-by-me studies of this out there…)

Lastly, there is a factor we always have to contend with when discussing environmental change, and that is adaptation. The experiments I’ve cited so far examine the reactions of individual organisms to changed circumstances, but the real change is occurring over a time scale of many generations for many of these creatures. As soon as you have such generation-spanning processes, evolution becomes a player. Will ocean calcifiers be able to adapt? Are there ways to predict which of them will?

There’s exactly one title in my reference manager that deals with that sort of thing, a breeding experiment/simulation study about a sea urchin and a mussel population by Sunday et al. (2011), but again, that paper points out how the ability to adapt will be highly dependent on the genetic variation present in a population. Genetic variation is not just species-dependent, it varies even within a species unless the entire species is one interconnected population (which does happen sometimes, see the recent news about giant squid). And there are many, many species in the ocean. Most of which we probably haven’t even seen, let alone studied.



Byrne M et al. (2011) Unshelled abalone and corrupted urchins: development of marine calcifiers in a changing ocean. Proceedings of the Royal Society B 278:2376-2383

Cameron CB & Bishop CD (2012) Biomineral ultrastructure, elemental constitution and genomic analysis of biomineralization-related proteins in hemichordates. Proceedings of the Royal Society B 279:3041-3048

Cooper TF et al. (2012) Growth of Western Australian corals in the Anthropocene. Science 335:593-596

Feely RA et al. (2001) Uptake and storage of carbon dioxide in the ocean: the global CO2 survey. Oceanography 14:18-32

Kroeker KJ et al. (2010) Meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms. Ecology Letters 13:1419-1434

Miller AW et al. (2009) Shellfish face uncertain future in high CO2 world: influence of acidification on oyster larvae calcification and growth in estuaries. PLoS ONE 4:e5661

Ries JB et al. (2009) Marine calcifiers exhibit mixed responses to CO2-induced ocean acidification. Geology 37:1131-1134

Sunday JM et al. (2011) Quantifying rates of evolutionary adaptation in response to ocean acidification. PLoS ONE 6:e22881

Venn AA et al. (2013). Impact of seawater acidification on pH at the tissue–skeleton interface and calcification in reef corals. PNAS 110:1634-1639

Wood HL et al. (2008) Ocean acidification may increase calcification rates, but at a cost. Proceedings of the Royal Society B 275:1767-1773

If only!

Ah, abstracts. Because the world has no attention span, and there isn’t enough time in the universe to read every new paper relevant to your research anyway, we need abstracts in front of scientific articles. Heck, if you are anything like me – and I’m told this is a general scientist thing, not just my laziness – it’ll be an especially important paper indeed that you actually read in full. (Well, that or especially bloggable.)

So you write abstracts to sell your stuff, because abstracts are all most people will ever see of your work. And in your effort to sell your stuff, you sometimes end up writing total fucking nonsense. Probably without even noticing it. (I like to assume the best about people.)

Like, for example, where Mu et al. (2013) write in the abstract of their recent study about regenerating fingers in mice that…

The differences between amphibian regeneration and mammalian wound healing can be attributed to the greater ratio of MMPs to TIMPs in amphibian tissue.

To make the above sound less like a foreign language: MMPs [= matrix metalloproteinases] are protein-chomping enzymes that modify the extracellular matrix that surrounds and connects cells in a tissue. TIMPs [= tissue inhibitors of MMPs] are proteins that interfere with their function. And yes, MMPs are important for regeneration… but if the difference between the amazing leg-regrowing abilities of newts and mammals’ almost complete failure to regenerate even one puny finger were that simple, we would have eradicated one-armed bandits long ago.

If only it were that simple!

(Remind me to make fun of my own papers if/when I ever get something published. I kinda feel bad for nitpicking other people’s language as if I never wrote anything stupid… >.>)



Mu X, Bellayr I, Pan H, Choi Y, Li Y (2013) Regeneration of soft tissues is promoted by MMP1 treatment after digit amputation in mice. PLoS ONE 8:e59105

Lotsa news

Hah, I open my Google Reader (damn you, Google, why do you have to kill it??? >_<), expecting to find maybe a handful of new articles since my last login, and instead getting both Nature and Science in one big heap of awesome. The latest from the Big Two are quite a treat!


By now, of course, the internet is abuzz with the news of all those four-winged birdies from China (Zheng et al., 2013). I’m a sucker for anything with feathers anywhere, plus these guys are telling us in no uncertain terms that four-wingedness is not just some weird dromaeosaur/troodontid quirk but an important stage in bird evolution. Super-cool.


Then there is that Cambrian acorn worm from the good old Burgess Shale (Caron et al., 2013). It’s described to be like modern acorn worms in most respects, except it apparently lived in a tube. Living in tubes is something that pterobranchs, a poorly known group related to acorn worms do today. The Burgess Shale fossils (along with previous molecular data) suggest that pterobranchs, which are tiny, tentacled creatures living in colonies, are descendants rather than cousins of the larger, tentacle-less and solitary acorn worms. This has all kinds of implications for all kinds of common ancestors…


Third, a group used a protein from silica-based sponge skeletons to create unusually bendy calcareous rods (Natalio et al., 2013). Calcite, the mineral that makes up limestone, is not normally known for its flexibility, but the sponge protein helps tiny crystals of it assemble into a structure that bends rather than breaks. Biominerals would just be ordinary rocks without the organic stuff in them, and this is a beautiful demonstration of what those organic molecules are capable of!


And finally, Japanese biologists think they know where the extra wings of ancient insects went (Ohde et al., 2013). Today, most winged insects have two pairs of wings, one pair on the second thoracic segment and another on the third. But closer to their origin, they had wing-like outgrowths all the way down the thorax and abdomen. Ohde et al. propose that these wing homologues didn’t just disappear – they were instead modified into other structures. Their screwing with Hox gene activity in mealworm beetles transformed some of the parts on normally wingless segments into somewhat messed up wings. What’s more, the normal development of the same bits resembles that of wings and relies on some of the same master genes. It’s a lot like bithorax mutant flies with four wings (normal flies only have two, the hindwings being replaced by balancing organs), except no modern insect has wings where these victims of genetic wizardry grew them. The team encourage people to start looking for remnants of lost wings in other insects…

Lots of insteresting stuff today! And we got more Hox genes, yayyyy!



Caron J-B et al. (2013) Tubicolous enteropneusts from the Cambrian period. Nature advance online publication 13/03/2013, doi: 10.1038/nature12017

Natalio F et al. (2013) Flexible minerals: self-assembled calcite spicules with extreme bending strength. Science 339:1298-1302

Ohde T et al. (2013) Insect morphological diversification through the modification of wing serial homologs. Science Express, published online 14/03/2013, doi: 10.1126/science.1234219

Zheng X et al. (2013) Hind wings in basal birds and the evolution of leg feathers. Science 339:1309-1312

Jelly babies, dead and pretty

Is it really, really wrong to find pictures of dead baby animals adorable?

OK, the animals in question are sea anemones and jellyfish, but I still feel kind of perverted for the sentiment. But seriously, look at this young polyp of a starlet sea anemone (stained blue because the point of this image was the expression of the muscleLIM2 gene, not the cuteness of the creature ;)):


It looks like a little slug! D’awwww!

(I think I may be reading too much Featured Creature… ^.^;)

And then there’s this baby jellyfish, with fluorescent stains for actin protein and cell nuclei…


… or a field full of poppies, depending on your point of view! 😀

[Both images are from the supplementary figures of Steinmetz et al. (2012), Nature 487:231-234.]

“Same” function, but the devil is in the details.

Aaaaaand todaaaaay, ladies and, um, other kinds of people…. Hox genes!

Considering that I did my Honours project on them and I think they are made of awesome, I’m kind of shocked by the general lack of them here*. Hmmmmmm. Well, having just found Sambrani et al. (2013), I think today is a good time to do something about that.

Hox genes in general are “what goes where” type regulators of development. In bilaterian animals, they tend to work along the head to tail axis of the embryo. (Cnidarians like sea anemones also have them, but the situation re: main body axis and Hox genes in cnidarians is a leeeetle less clear. And heaven knows what sort of weird things happened with the rest of the animals.)

Hox genes are responsible for one of the peculiarities of the insect body plan. Unlike many other arthropods, insects have leg-free abdomens. On the left below is a poor little lobster with legs or related appendages all the way down (plus a bonus clutch of eggs). (Arnstein Rønning, Wikimedia Commons). To her right is a bland, boring insect abdomen (Hans Hillewaert, Wikimedia Commons).

As I said, Hox genes are responsible for the difference. Three of them are expressed in various segments of the abdomen of a developing insect: Ultrabithorax (Ubx), Abdominal-A and Abdominal-B. I’m going to whip out that amazing fluorescent image of Hox gene expression in a fruit fly embryo from Lemons and McGinnis (2006) because aside from being cool as hell, it also happens to be a good illustration:

(The embryo is folded back on itself, so the Abd-B-expressing tail end is right next to the Hox gene-free head)

In insects, all three can turn off the expression of the leg “master” gene distal-less (dll). However, they turn out to do so through two different mechanisms. Ubx and Abd-A proteins have long been known to team up with the distantly related Extradenticle (Exd) and Homothorax (Hth). With their partners, the Hoxes can sit on a regulatory region belonging to the dll gene and prevent its activation.

Sambrani et al. were curious whether Abd-B works in the same way. Sure enough, Abd-B also represses dll wherever it shows up. However, when it comes to interacting with Exd and Hth, differences start to emerge. For starters, those two aren’t even present in the rear end of the abdomen, where Abd-B does its business. When the researchers took the regulatory region of dll and threw various combinations of proteins at it, they found that (1) Abd-B is perfectly capable of binding the DNA on its own, (2) Exd, Hth or engrailed (another Hox cofactor) didn’t improve this ability at all, (3) Hth alone or in combination with the others actually inhibited the binding of Abd-B to the dll regulatory sequence.

Interestingly, dll repression in the anterior and posterior abdominal segments requires the exact same bits of regulatory DNA even though different proteins are involved. It looks like in the posterior segments, Abd-B actually takes over an “Exd” binding site – maybe that’s how it can do the job without getting Exd itself involved.

Furthermore, while the DNA-binding ability of Abd-B is crucial to its ability to kill dll expression, the same is not the case for Ubx. The authors speculate that cooperation with Exd and Hth kind of exempts Ubx from having to bind the regulatory sequences itself, while Abd-B, being on its own, can’t afford to slack off like that. The paper illustrates the idea with such a deliciously ugly pair of drawings that I feel compelled to post it:

(I know they’re going for colour-matching with the fluorescent images, but unfortunately glowy greens and reds that look good on a black background kind of just hurt my eyes on white.)

I don’t really have a point to make here. (There doesn’t always have to be a point, right?) There’s absolutely nothing surprising about the fact that different Hox genes evolved the same overall function in different ways –  after all, they existed as separate entities long before insects lost their buttward legs. I just think Hox genes are cool, and this was an interesting look into the nuts and bolts of how they work. And that’s that.



*Well, aside from this one I’ve written three posts about them and a couple more where they are mentioned. That’s maybe not that bad considering how many different things I’m interested in.



Lemons D and McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313:1918-1922

Sambrani N et al. (2013) Distinct molecular strategies for Hox-mediated limb suppression in Drosophila: From cooperativity to dispensability/antagonism in TALE partnership. PLoS Genetics 9:e1003307.