Superfood shelf. Just-fucking-what.

After feeding every stupid health scare ever with its “free from” labels, Tesco has reached a new low. Or maybe it reached it long ago and my brain just refused to see it.

The damn place has a SUPERFOOD SHELF now. Because salad can’t just be healthy, it has to be SUPER healthy.

Image0059

Urgh.

I have to go and do some real science now.

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The post-eating monster

This is the second time I wrote an entry, pressed publish, and ended up publishing a completely empty post. Why is this thing eating my carefully written blathers?

At least last time I had a saved version I could start again from. This one just disappeared into the aether.

I am sad and pissed and all kinds of grumpy now. Probably not a good time to ask tech support about the problem.

I might be back once I stopped screaming obscenities inside my head.

Living jellyfish =/= earliest stage in metazoan evolution…

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

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

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

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

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

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

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

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

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

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

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

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

*goes away to growl quietly*

***

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

***

Reference:

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

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… >.>)

***

Reference:

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

For fuck’s sake, scientists!

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

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

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

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

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

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

srivastava_fig2_183mm

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

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

Now, which is the basal lineage?

The correct answer is “relative to what?”

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

Basal lineage” depends on your point of view.

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

SperlingSponges

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

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

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

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

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

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

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

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

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

***

References:

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

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

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

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

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

Interpreting ‘omics: a good example this time

Remember how I complained that people often seem to forget the scientific method when it comes to transcriptomics? Well, I’m glad to say some scientists still remember those all-important steps between data and conclusion. When looking at the predicted functions of the genes active in these cute little baby worms* during the first three days of their lives, Kenny and Shimeld (2012) not only compared their data to a “background” dataset from a well-studied animal, but also

  • did statistical tests to confirm that the differences they saw were real,
  • discussed several possible causes for them.

… including those that weren’t biologically interesting at all, like limitations of their methods. In the end, they couldn’t really draw strong conclusions from this particular part of their analysis, but the best thing is they sound perfectly aware of the difficulty and careful not to go too far in interpretation.

Folks, this is how you should write a transcriptomics paper. Not look at a few out-of-context numbers and concoct a story around them.
***

*Okay, am I the only one who finds trochophores adorable? :$

***

Reference:

Kenny NJ & Shimeld SM (2012) Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida: Serpulidae) reveals annelid trochophore transcription factor cassette. Development Genes & Evolution Online First™ article available online 8/10/2012, doi: 10.1007/s00427-012-0416-6

Did Not Do the Research

Maybe a random rant is not the best way to break a longish silence, but I just had to. Because WTF, Budapest Zoo?

Preamble: the aforementioned is an amazing place. I’d never recommend anyone not to visit if they got the chance. But sometimes, institutions of public education fail rather spectacularly at actually educating the public. And nothing gets me quite like “education” spreading misinformation. I didn’t rant about the painful-to-read evolution stuff I saw at London Zoo a while back, mainly because I couldn’t be bothered to thoroughly fact-check all of my million and one objections. But this, this is so annoyingly simple. And so infuriatingly wrong.

I’m referring to this:

It’s supposed to be an Oviraptor with its adorable chicks. Now, me and anatomy in general are very distant acquaintances, but surely even the last stubborn holdouts of Jurassic Park fandom have heard of feathered dinosaurs by now. Surely someone designing an exhibit/sculpting a dinosaur for a big-ass zoo would know, or find out in the course of their in-depth research that in all likelihood, everything closer to birds than, say, Allosaurus was at least a little bit fuzzy, and an Oviraptor-grade animal definitely bore feathers. Come the fuck on, surely they’ve at least heard of Caudipteryx?

The sculpture is also bunny-handed. I’ve spent enough internet time around hardcore dinosaur nerds to know that these creatures couldn’t hold their forelimbs like that without seriously damaging something. Unlike us, they couldn’t pronate their forearms. Maybe this arcane piece of information isn’t easily available outside dinosaur nerddom? But one would think that someone preparing an educational exhibit would, you know, do some research about the animals in question.

The whole fuck-up is all the more puzzling because right next to this monstrosity you find these:

Which also aren’t the best works of dinosaur art I’ve seen by a long shot, but at least they don’t look like they time-travelled from the eighties. If the “raptors” got the updated treatment, why was poor Oviraptor left behind?

Have a goddamned null hypothesis!

I’m in the middle of Joubert et al. (2010), and I’m shaking my head a bit.

The paper is a pretty standard specimen of the kind of next-generation sequencing study that’s been proliferating in recent years. It looked for genes that make the shell of an oyster by sequencing all the RNA expressed in the tissues that build the shell.

This sort of study generates an awful lot of data, which makes it unfeasible to analyse it just by old-fashioned human brainpower and maybe a little statistics. Anyone happy to manually trawl through nearly 77 thousand sequences to find the interesting ones is a lot crazier than anyone I know… and anyone willing to study each of them to figure out what they do is probably a god with all of eternity at their hands.

One of the ways researchers use to quickly and automatically find interesting patterns in such large datasets is the Gene Ontology (GO) database. GO uses a standard vocabulary to tag protein sequences with various attributes such as where they are found within the cell, what molecules they might bind to, and what biological processes they might participate in. Such tags may be derived from experiments, or often from features of the sequence itself. For example, proteins often contain specific sequence motifs that tell the cell where to send them. Assuming that related proteins have similar functions in different organisms, GO annotations derived from one creature can be used to make sense of data produced in another.

So, Joubert et al. took their 77 thousand sequences, translated them into protein, and ran them through a program that finds similar sequences with existing annotations from GO or similar databases. They got some numbers. X per cent of the proteins are predicted to have some metabolic function, Y per cent of them bind to something, and so on. Then they went on to pull hypotheses out of these numbers. And that’s where they really should have remembered Scientific Method 101.

The part where I started looking askance at the paper is where they get excited about the percentage of predicted ion-binding proteins in the dataset. Of course, oyster shells are largely made of ions (calcium and carbonate ions, to be precise). But, importantly, “ions” are an awfully broad category, and they are essential for many of the everyday workings of any cell. Even calcium ions, which make up one half of the mineral component of the shell, play many other roles. Muscle contraction, cell adhesion, conduction of nerve impulses – all involve calcium ions in one way or another, and lots and lots of proteins either regulate or are regulated by calcium signals via binding the ions. So the question arose in my head: is it really unusual for 17% of “binding” sequences in a sample to bind ions?

This is not the first time I see that people who publish high-throughput sequencing data don’t ask that sort of question. They just report the pattern they saw, and try to interpret it. But patterns can only be interpreted in context. To tell whether a pattern is unusual, you must first know what the usual pattern looks like!

In fact, finding this many ion binding proteins doesn’t seem extraordinary at all. SwissProt, the awesome hand-curated protein sequence database, has a really handy browsing tool where you can get a breakdown of a selected set of sequences by GO categories. Curious, I had a quick look at all the 20 244 human proteins in SwissProt. (I picked humans because I’d probably be hard-pressed to find organisms with more GO-annotated proteins.) Out of the 11 674 that GO classifies under “binding”, 3934 are thought to bind ions. That’s almost 34%. This almost certainly has nothing to do with us having bones made of ions – SwissProt includes proteins from all tissues.

Even when you compare ion-binding sequences with ones that are predicted to bind something else within the same dataset, the “background” wins: while the human collection I looked at has about 1.6 times as many protein-binding sequences as ion-binders, in the oyster dataset the protein-binders outnumber the ion-binders two to one. Caveats apply as usual – datasets are incomplete, GO annotations are probably both incomplete AND a bit suspect, etc.; but I can’t see how that justifies the implication that the pattern this study found in the oyster is somehow special and interesting from a shell-building perspective. The whole thing smells like looking for faces in the clouds to me. Science is not simply about pattern-finding – it’s about finding meaningful patterns. I hope that this crucial distinction doesn’t get completely washed away by the current flood of data, data, data.

***

References:

Joubert C et al. (2010) Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization. BMC Genomics 11:613

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

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

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

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

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

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

This is why I was madly happy to find this:

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

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

Much ado about nothing

I am disappointed.

I have a soft spot for Kimberella, one of the few Precambrian animals that we can identify with reasonable precision. (Not to mention its pretty name! :D) Our love affair started before I became involved with biomineralisation, which might have contributed to the fact that I totally overlooked Ivantsov (2009).

(Image: Ivantsov’s Kimberella, rendered by the masterful hands of Nobu Tamura. From Wikipedia.)

The paper shows up on Kimberella‘s lovely Wikipedia page as a citation for the following:

The deformation observed in elongated and folded specimens illustrates that the shell was highly malleable; perhaps, rather than a single integument, it consisted of an aggregation of (mineralized?) sclerites.

These days when I’m >this< close to dreaming about biominerals at night, this jumped out at me like a giant neon sign. What? A mineralising animal that old? (I think this was also before I saw Coronacollina.) So I downloaded the paper, and eventually got round to reading it, and…

Pfft.

It’s an alright piece of scientific literature, and it’s got lots of lovely pictures of Kimberella fossils (though Fedonkin et al. [2007] already had a ton of those). I would have been happy about it but for the fact that it totally flopped on the mineral thing. I thought that, you know, Ivantsov had some evidence to suggest that those bumps on the creature’s back were originally made of mineral stuff. And, indeed, his abstract quite confidently states not only that they were mineralised but also the specific mineral:

The fossil material shows that Kimberella had hard sclerites, probably of aragonite…

His reasoning? Let me quote…

The alternation of nodes and coarse folds in the central zone of the fossil may be explained by assuming that the nuclei of nodes were clumps of hard substance, which rapidly destroyed after the death of the animal. Aragonite, which obviously had no chances to be preserved in the terrigenous sediment, which, in addition, was saturated with hydrogen sulfide (Gehling, 2005), could have been such a substance.

I mean, really? They “could have been” made of aragonite because they disappeared? It’s like there is no other tough-ish material that can be destroyed after an animal dies. And he doesn’t go any deeper than that – no discussing/excluding other possibilities, nothing. He just leaves it there.

People, can you please not claim things in your abstracts that you then barely discuss, let alone demonstrate, in the paper?

***

References:

Fedonkin MA et al. (2007) New data on Kimberella, the Vendian mollusc-like organism (White Sea region, Russia): palaeoecological and evolutionary implications. In: Vickers-Rich P & Komarower P (eds). The Rise and Fall of the Ediacaran Biota. Geological Society, London, Special Publications 286:157-179

Ivantsov YA (2009) New reconstruction of Kimberella, problematic Vendian metazoan. Paleontological Journal 43:601-611