The unexpected complexity of nothing

I don’t think I’ve covered anything theoretical in a while, so here’s an interesting modelling study that I’ve just come across in PNAS (Shah et al., 2015). It discusses a key point in evolutionary theory – that “mutations” and “fitness” don’t exist in a vacuum. More specifically, it investigates how mutations that have little effect on fitness at the time interact with other mutations in a protein under strong purifying selection. Lots of studies deal with the role of interactions (or epistasis) between mutations in adaptation and innovation, but apparently, the question is much less explored when selection is keeping things the way they are.

Shah et al.’s approach is a mixture of theory and empirical data. The protein they consider is perfectly real – it’s the amino acid-binding protein argT from the bacterium Salmonella typhimurium (yep, that salmonella), and it was chosen because its structure is well-known and relatively simple. In contrast, the mutations happen entirely on a computer, although the models used to calculate their fitness effects in a simulated population of bacteria were calibrated to match the real-world distribution of the effects of mutations under similar circumstances.

The most important of these circumstances is the fact that this protein is not actively adapting to anything. It is already well-adapted to its function, and there is nothing pushing it in a new direction. Nonetheless, mutations happen whether or not they are needed; what the authors wanted to know is whether the mutations that arise in this environment constrain the course of evolution.

The researchers took the real argT protein sequence and introduced changes. In each round, ten random mutations were proposed, only one of which made it into the next round. For each proposed mutation, they used a program designed to model protein structure to calculate the stability of the new protein. Proteins are long chains of amino acids twisted and folded into specific 3D shapes. The stability of these shapes is important because a protein that is too rigid or too floppy can’t bind the right molecules with the right strength (remember, the function of argT is to grab certain amino acids).

The simulations assumed that the real protein is pretty much optimally stable already, and either increased or decreased its stability would decrease its fitness*. Protein stability was converted to fitness in a way that a realistic percentage of mutations were neutral, kinda bad or plain lethal (you can’t have beneficial mutations here, since the original protein is assumed to be optimised for its function). Finally, the least bad mutation in each round was chosen to update the protein sequence. This procedure was repeated until the protein had accumulated 30 changes, and the whole process was replicated 100 times.

With a hundred new virtual proteins in hand, the really interesting part of the experiment could begin. The grand aim of this whole study was to examine mutations in their historical context. All mutations that were added to the original argT sequence were neutral or nearly neutral at the time of their introduction – but would they be neutral if they were introduced at an earlier point in the evolutionary sequence? And would they still be neutral, or rather, reversible, after a bunch of other mutations had accumulated on top of them?

As you may have guessed, the answer to both questions is no. Even though the final 100 proteins were pretty much as good as the original, and each of the mutations that made it through had close to zero effect on fitness at the time, taking mutations out of their context and sticking them into different backgrounds showed that their lack of effect was highly contingent on the history of that particular sequence.

The graph below summarises what happens if you take mutation 16 and either shift it to an earlier point, or take it out at a later point (a similar pattern holds no matter which mutation you start from). On the vertical axis is the fitness effect of the same mutation at different points relative to its effect at the time it actually occurred. The left side of the graph is consistently below zero – at any point before its “proper” time, mutation 16 would have been more deleterious. It only worked with all 15 previous mutations already in place.

Shah_etal2015-contingency.large

On the right side – mutation 16’s future – fitness effects rise rapidly. The more new mutations are added, the more “beneficial” (or more precisely, irreversible) mutation 16 becomes. Even though it didn’t do much at the time, as soon as other mutations come to rely on it, you can’t take it out without royally screwing up the whole protein. The mutation has become entrenched, to use the authors’ terminology. This figure is an average of all 100 simulations; the results are pretty consistent.

Of course, there are some caveats. One of the most important is that in real populations, mutations are not necessarily fixed one at a time, and the way multiple co-existing mutations interact could be quite different from the way individual mutations affect subsequent individual mutations. Another big if is the accuracy of the software that calculates protein stability – getting from protein sequence to structure and physical/chemical properties is still notoriously difficult. In this study, considering only the first few mutations in each series (i.e. before the virtual protein diverged too far from the original with known properties) doesn’t change the main results, so the authors don’t think this is a major problem for their conclusions. There is also the fact that global protein stability, the variable used here to estimate fitness, is not the same thing as function (in this case, binding specific amino acids). However, the latter depends only on a tiny proportion of the larger structure, so global stability is probably a reasonable proxy.

It occurs to me that what Shah et al.’s study simulated is basically the evolution of irreducibly complex nothing. Here we have a protein that does the exact same thing its ancestor did (with the above caveat) despite having a rather different sequence. This utter lack of change evolved one tiny step at a time; each step dispensable, each step insignificant. Yet try to take out any of the earlier steps from the final product, and the whole edifice collapses.

Call me strange, but I find this… amusing.

***

*They actually repeated the entire experiment with an alternative assumption that increases in stability are neutral rather than deleterious, but they got very similar results, largely due to the fact that very few mutations actually increased the stability of argT.

***

Reference:

Shah P et al. (2015) Contingency and entrenchment in protein evolution under purifying selection. PNAS 112:E3226–E3235

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Msp130 adventures, or the Mammal does science

I’ve been writing this blog almost since I started my PhD, but the closest I actually got to writing about my own work was a long fangirl squee about fan worms. Most of my project involved describing some really basic things about a relatively unknown animal, and probably not terribly interesting unless you’re an expert in my field (also, my brain is convinced that nearly everything I do is shit, so I don’t particularly like talking about it…). However, I do have this cool little story I’ve been burning to tell the world, and couldn’t because we wanted it published… Now it is (Szabó and Ferrier [2015]; there goes my super-secret identity, I suppose 😉 )

My story involves a family of proteins called msp130. I wish they had a more fun name than that, but they were named by sea urchin people, and unlike the fruit fly community, they don’t really seem to care about making their gene names fun. (Msp130 stands for “mesenchyme-specific protein, 130 kDa”, in case you wondered; kDa, kilodaltons, being units of molecular mass.)

It all started with a sea urchin

The original msp130 was discovered in sea urchin larvae. It is found in – or rather, on the surface of – primary mesenchyme cells (PMCs), a specialised population of cells that build the calcareous skeleton of the larva. Here’s a photo of a sea urchin embryo with PMCs stained blue, from Illies et al. (2002). At this stage, the embryo is basically a squashed ball with a hole through most of it; the hole is going to become the gut, and its opening is the future anus.

Illies_etal2002-msp130r2_gastrula

Here’s a polarised light photograph of an older larva of a sea biscuit. The skeleton is pretty much the only thing you can see, highlighted in stunning rainbow colours due to the birefringence of the mineral (Bruno Vellutini, flickr):

Msp130 turned out to be essential for skeleton formation – when researchers blocked its surface with antibodies, PMCs cultured in a dish couldn’t take up calcium and couldn’t make spicules (Carson et al., 1985; Anstrom et al., 1987). Not quite so long ago, Illies et al. (2002) found that S. purpuratus has at least three msp130 genes, and in the embryo/larva, the other two are also exclusively expressed in PMCs. This is what the first picture above shows: the blue stain appears in cells that express one of the msp130-related genes.

Anyway. A few years later, after the sequencing of the S. purpuratus genome, it turned out that there were at least seven such genes, residing in a couple of clusters in the genome (Livingston et al., 2006). However, until very recently, the msp130 family was only studied in echinoderms.

Horizons are expanded and weirdness is found

BUT, this being the genomic era, sea urchin guru Charles Ettensohn wanted to know more about these buggers – just how common are they? Where do they come from? Are they always lurking in genomes that have to produce calcified skeletons? What he found in sifting through the vast repository of sequence data that is Genbank was very interesting and somewhat puzzling: across the entire tree of life, msp130 genes only seemed to be present in echinoderms, acorn worms, lancelets, molluscs, a handful of algae… plus loads of bacteria and archaea (Ettensohn, 2014). There was no mistaking it: to someone accustomed to comparing protein sequences, the bacterial sequences very clearly were the same thing as the ones from animals and algae.

So, Ettensohn concluded, it looks like animals (and algae) probably didn’t inherit this thing directly from their common ancestor with other life forms. That would imply a lot of independent losses, and Occam’s razor dictates that we shouldn’t postulate so many hypothetical events without good reason (although, as Maeso et al. [2012] point out, animal genomes don’t seem to be quite as keen on Occam’s razor as scientists).

Instead, supposing that animals and algae repeatedly acquired these genes by horizontal gene transfer from bacteria (or each other?) seems like a simpler explanation. At least one loss probably did occur – among deuterostomes, vertebrates and sea squirts are the odd ones out in not having msp130 genes, and the most Occamific explanation of that pattern is that we just mislaid them somewhere along the line. Here’s a graphical representation of Ettensohn’s scenario from his paper – “HGT” stands for horizontal gene transfer events, and grey circles are meant to represent the extra msp130 genes that later evolved in each lineage by gene duplication:

Ettensohn2014-animalMsp130

However, Ettensohn also pointed out that whole genome-level information about most animal groups is still pretty thin on the ground (seriously, everyone, stop sequencing more stupid vertebrates. We’re all the same.) We don’t, for example, have published genomes from calcareous sponges, or from annelid worms who build calcareous tubes or have other calcareous hard parts. Like my wormies. And here’s where I come in – I happen to have a decent amount of transcriptome data (alas, no genome) from just the right kind of annelid. Better, my data are derived specifically from an organ with calcareous parts (the operculum – see my fanworm post).

Naturally, as soon as I read Ettensohn’s paper, the first thing I did was grab the sequence of the “original” msp130 protein and search my own data for a match. Ettensohn said that msp130 sequences were very easy to recognise… And yep, they are. With not much effort at all, I found a lovely, full-length msp130-like sequence in my big pile of data. Much as I hate doing molecular biology, I also managed to confirm the presence of the messenger RNA (or at least the presence of one end of it) in an actual test tube of actual RNA taken from the operculum. But that’s not really saying much re: the whole gene thievery issue – yeah, another animal fairly closely related to molluscs has an msp130 gene, and it’s active somewhere within a millimetre of a calcareous hard part. That, unfortunately, says precisely bugger all about their evolutionary origin.

But I had an idea, peeps. Introns!!!

Genes in pieces make answers come together

There is an important difference between the genes of prokaryotes like bacteria and eukaryotes like algae or animals. In the former, most genes are uninterrupted stretches of DNA. A bacterial gene is transcribed into messenger RNA, and everything in that mRNA that stands between the “start protein” and “end protein” signals is translated into a protein using the appropriate genetic code.

Most of the genes of eukaryotes, however, consist of chunks that encode parts of the protein product (exons) interrupted by chunks that get discarded during or after transcription (introns)*. So there’s a potentially easy way of telling whether a gene in two different animals came from their common ancestor or from some overly generous microbes. If they have introns in matching locations, that’s not a similarity they could have acquired just by getting the gene from the same bacterium!

I say potentially easy for at least two reasons. One, while some gene families keep their introns in the same places for a very long time, introns can come and go in evolution. They can even disappear completely under some circumstances, although something the size of msp130 does usually have at least a few. If msp130 genes have fast-evolving structures, we may not be able to tell whether molluscs and deuterostomes acquired them independently, or whether the positions of introns just changed too much since their common ancestor.

Two, introns can theoretically evolve twice in the same place – just as some parts of a genome can be hotspots for mutations, parts of a gene can be hotspots for new introns. Of course, the more similar the overall structure of two genes, the less likely “intron hotspots” become as an explanation.

I compared the exon-intron structures of all msp130 genes in a few representative species with sequenced genomes in which Ettensohn found such genes. Besides sea urchins (which are from one of the two main deuterostome lineages), I chose lancelets (from the other great branch of deuterostomes) and limpets (which are molluscs). Together, these three creatures represent all major animal lineages in which msp130 genes have been found. Alas, I couldn’t do it with my own animals, because I don’t have a genome to play with 😦 . I also checked all three algae – the two green algae on Ettensohn’s list are fairly closely related, but the third one is a brown alga separated by upwards of a billion years.

As I said, all of these species have fully sequenced genomes, but you really need two sources of data to do this kind of thing properly. A genome sequence includes the complete gene with all the introns – but without the corresponding mRNA sequences, we must use clever computer programs that search for characteristic DNA motifs and/or sequence similarity to other organisms to predict where introns begin and end. Aside from clever programs occasionally being remarkably stupid or getting confused by sequencing errors, you can hopefully see how relying on similarity doesn’t exactly provide unbiased evidence for my purposes.

Sequences derived from transcripts only contain exons, however, and not because a computer predicted them, but because they’re read from the fully edited mRNA. So aligning transcripts with genomes should tell you exactly where the introns are, although transcript data were incomplete or altogether missing for some of the genes I looked at. (I didn’t have that problem with sea urchins – Tu et al. [2012] helpfully sequenced transcripts of pretty much all urchin genes and uploaded the results to the genome browser.)

Nonetheless, the data that did exist told us enough to doubt Ettensohn’s idea. Importantly, I found enough to piece together the entire protein-coding portion of the mRNA for two of the limpet msp130 genes – in other words, the animals that Ettensohn thought likely to have acquired the family independently from sea urchins. In total, the animal species I investigated share not just one or two but seven intron locations (an msp130 gene has maybe a dozen introns altogether). One of those is also present in the algae, and the sequence next to it is almost identical across all of the genes. There’s really no mistaking that one! A few more introns are in generally similar locations, though they don’t line up perfectly in my best alignment**.

What can we conclude from this? I think we can probably say with reasonable certainty that deuterostomes and molluscs didn’t get msp130 genes from bacteria separately. Given the similarity with algae, they might not have got it from bacteria at all, although one similarly positioned intron is a lot easier to explain away as convergent evolution.

As I see it, either the last common ancestor of molluscs+annelids and deuterostomes had msp130 genes and only a few of its descendants kept them, or one of the two lineages snatched it from the other after those seven introns had originated. (Animals stealing genes from other animals is relatively uncommon, as far as I know.)

…some answers, anyway…

If you put the evidence for a single origin together with the incredibly gappy distribution of this gene family, the other side of the equation is a ridiculous number of losses. Why? And what’s the deal with msp130 and calcification? Is there a deal at all? Ettensohn speculated that acquiring msp130 might have had something to do with acquiring calcareous skeletons – did it?

IMO we really don’t have enough examples to properly assess this association, and my impression is that we actually know very little about the roles of these genes. Oh, we know that some of them are pretty specific to calcification in certain echinoderms, and they seem to be around in multiple organs in molluscs given that the hundreds of RNA sequences I found had been extracted from anything from gonads to mouthparts. And, of course, at least one of them is doing something in a partly calcified body part in my annelid, though we haven’t yet checked exactly where or what.

But calcification is pretty much the only context in which msp130s have been investigated; since everyone thought they were just echinoderm “calcification genes”, no one thought to look elsewhere. What do they do in, say, lancelets, which have six of the genes but not much of a calcified skeleton that we know of? Lancelets may well have something calcareous that isn’t a skeleton – other animals with no obvious calcareous skeletons, such as arachnids or earthworms, produce little calcareous granules that might work to store calcium or get rid of a surplus. Most of the limpet transcripts I found come from testicles or ovaries, which don’t tend to calcify, but gonads are a bit special and turn on lots of random genomic shit that may or may not actually have a function. AFAIK, none of the three algae from which msp130 genes are known has a calcareous skeleton, but many other algae do.

In summary, I did some detective work and discovered something and I feel rather clever about all of that, but in the process I learned just how much more we don’t know about this obscure but intriguing little gene family.

… actually, that sounds like a fairly typical summer in science. 🙂

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*Don’t ask me how that happened (it’s not even remotely my area), but now that the system exists, it does enable eukaryotes to make loads of different proteins from a single gene just by picking and choosing which exons to keep. See fruit fly Dscam, or the “brutally murdering the one gene, one protein hypothesis, forty thousand splice variants at a time” gene. Introns can also contain a variety of regulatory sequences that determine either the behaviour of their own gene or even that of a different gene, so introns are far from useless. They’re just a bit… counterintuitive.

**Aligning similar sequences is part science, part art. Often, there’s no single clear best way to align two or more genes or proteins; the various programs people have written for this job will all come up with slightly different answers, and an experienced pair of eyes will probably want to tweak all of them. Whether introns are really in the same place in two genes can therefore be a bit ambiguous, depending on the degree of sequence similarity.

***

References:

Anstrom JA et al. (1987) Localization and expression of msp130, a primary mesenchyme lineage-specific cell surface protein in the sea urchin embryo. Development 101:255-265

Carson DD et al. (1985) A monoclonal antibody inhibits calcium accumulation and skeleton formation in cultured embryonic cells of the sea urchin. Cell 41:639-648

Ettensohn CA (2014) Horizontal transfer of the msp130 gene supported the evolution of metazoan biomineralization. Evolution & Development 16:139-148

Illies MR et al. (2002) Identification and developmental expression of new biomineralization proteins in the sea urchin Strongylocentrotus purpuratus. Development Genes and Evolution 212:419-431

Livingston BT et al. (2006) A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus. Developmental Biology 300:335-348

Maeso I et al. (2012) Widespread recurrent evolution of genomic features. Genome Biology and Evolution 4:486-500

Szabó R & Ferrier DEK (2015) Another biomineralising protostome with an msp130 gene and conservation of msp130 gene structure across Bilateria. Evolution & Development 17:195-197

Tu Q et al. (2012) Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Research 22:2079-2087

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.

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References:

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

And now, a Coronacollina rant.

Coronacollina aside: great discovery + science communication fail = grumpy Mammal.

Now that we’ve drunk a few metaphorical beverages of choice to the melodiously named little sponge, allow me a rantish tangent on the terribly written press release that accompanies the paper. It makes me roll my eyes right off the bat by saying that “life” exploded in the Cambrian. No, no, no. Animals did. Plenty of other life forms didn’t, far as I know.

This, especially the part I bolded, just seems to come out of nowhere: “The finding provides insight into the evolution of life — particularly, early life — on the planet, why animals go extinct, and how organisms respond to environmental changes. The discovery also can help scientists recognize life elsewhere in the universe.” Excuse me, but where the fuck did that come from? Needless to say there’s not a word about extraterrestrial life in the entire paper, and not much about extinction or environmental change, either.

Then the article goes on to, well, not so much “suggest” as outright claim that no Precambrian animals with hard skeletons were known before this discovery: “’Up until the Cambrian, it was understood that animals were soft bodied and had no hard parts,’ said Mary Droser, a professor of geology at the University of California, Riverside, whose research team made the discovery in South Australia. ‘But we now have an organism with individual skeletal body parts that appears before the Cambrian.’” Cloudina and Namacalathus beg to differ, and I would bet money that Mary Droser knows this. In fact, Cloudina is referenced in the paper as an example of Precambrian hard parts. I’m undecided on what’s worse, if Droser fibbed about the fossil record, or if whoever edited her comments was clueless. And this is a fairly important piece of information, as the truth makes the significance of poor Coronacollina slightly less obvious. (Hmm…)

The next “highlight” (lowlight???) is where it says Coronacollina was constructed like Cambrian sponges. No, it was constructed like a Cambrian sponge, and an unusual one at that. There were many other Cambrian sponges that looked nothing like these prickly cones, see an assortment from the Burgess Shale here.

Then comes this characterisation: “[C. acula was s]haped like a thimble to which at least four 20-40-centimeter-long needle-like “spicules” were attached…” Um, someone didn’t read the paper here. It’s at most four in the known specimens, although the authors do speculate that there could’ve been more in life. And the lower end of their lengths has one fewer zero…

The crowning misreading near the end: “Droser explained that the spicules had to have been mineralized because the casts show they are ruler-straight. Moreover, they broke.” Dear article writer, I don’t know what she “explained” in person, but the paper describes the spicules (bolding mine) as “straight, rigid structures that were most commonly broken once disarticulated. Some spicules display a slight deviation from ruler-straight, implying either a composition of chitin that was plastic during life, or a mineralized composition of biogenic silica or calcium carbonate preserved deformed due to plastic behavior postburial” Newsflash: chitin is not a mineral. Granted, later in the paper they reason that some sort of mineral is most likely due to the apparent brittleness of the spicules, but they clearly don’t rule out a mainly organic composition.

Grah. I hate how press releases often get so many things wrong, and this one isn’t even a decent piece of writing. Disappointing doesn’t even begin to describe it.

Irrelevant?

Sometimes, renowned scientists say things that blow my mind.

I was reading this news article about a quantum physics experiment. It all seemed suitably exciting and mysterious to my lay eyes, and then the article hit me with this:

“Experiments are only relevant in science when they are crucial tests between at least two good explanatory theories,” [David] Deutsch says. “Here, there was only one, namely that the equations of quantum mechanics really do describe reality.”

I’m sorry, but that’s just… wrong. A lot of real-life experimental work involves testing a single idea against a null hypothesis (e.g. “this mutation causes disease A” vs. “this mutation doesn’t cause disease A”). And you don’t need two competing explanations for one explanation to turn out wrong (e.g. a particular mutation is the only cause you can think of for disease A, but then you find lots of people having the mutation but not the disease). Sure, QM has passed many, many tests – but remember, science can only ever say “this is right to the best of our knowledge”, not “this is Right”. As far as I understood the article, this experiment also looked at QM in a new way, so it’s not like it was a boring replication of something we’d seen a thousand times. Maybe Deutsch is right to question its importance, but I think he chose a really poor reason for doing so.

(Disclaimer: the quotes that appear in articles like this are not necessarily the words that came out of the interviewee’s mouth/keyboard. So like a good scientist, I’ll leave some reservations in my judgement there.)

Internet science gets it wrong

While I was writing the post about treehoppers, I went in search of a simple diagram of insect anatomy. One of the pictures that Google threw my way was the one here. From my limited experience, Earth Life Web isn’t bad in general, but  they got the wings of their generalised insect totally wrong. Insects (without exception AFAIK) have three thoracic segments, and the wings of flying insects are on the second and third. NOT the first and second, which is what the Earth Life diagram looks like.

Just goes to show that you have to be very, very careful when mining scientific information from the web. Or from anywhere else, really.