In which fangirling turns into philosophy

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

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In which I *don’t* blame journalists

Given the existence of this blog, you might have guessed that I’m interested in communicating science to a wider audience. Recently (well, in November) I went to one of Sense About Science‘s media workshops to learn more about science communication – specifically, about the representation of science in the media and issues surrounding same. When I’d digested the experience, I had some thoughts. Then I committed them to writing. Then the writing sat in a folder on my desk for half a year. I think it might just be time to publish it 😛

(Although this should go without saying, I don’t speak for all scientists. I have a personality and I have experiences, and both of those may distort my perspective. Read the following as my personal opinion.)

*

Once upon a time, I was a regular reader of ScienceDaily. It’s one of those places where science news gather, and I was interested in science news. I’d never been a big reader of other news, so it suited me perfectly.

Except I’m a pedantic nerd, and reading press releases can be… trying for my kind. I eventually got to the point of asking my supervisor how much scientists had to do with press releases of their papers, because so many of the ones I’d read on SD seemed to have been written by people who either wanted to blow everything out of proportion or simply had no clue.

The boss answered that the researchers would provide source material, but the press office write the actual release, and poor scientists can’t do a whole lot about its final incarnation. He made no secret of his dismissal of the press office, and opinionated little crusader that I am, I felt vindicated.

For a good long while, then, I felt completely justified in griping about journalists. They were, after all, churning out overblown claims and garbling perfectly good science to turn it into news. Was it a wonder, then, that so many people were becoming jaded and mistrustful of science? If you read articles touting miracle cures for cancer and marvelling at the biggest, oldest, most awesomest something ever, if every week decades-old paradigms seem to be turning on their heads, it isn’t at all surprising that you’d end up as some of my online discussion partners did. I saw these people, dismissive of science, firmly convinced that since science changes like the wind, it isn’t worth believing. Today’s knowledge will just become tomorrow’s outdated theory anyway. It infuriated me.

Sometimes, the scientists themselves seemed to be part of the problem. Remember “Ida,” the beautiful Eocene primate fossil? The sensational claims of her being a “missing link” in our own ancestry came from her describers, not their press offices. Likewise, the press release in which palaeontologist John Ruben was quoted as saying (to any vaguely well-informed dinosaur nerd) hugely outlandish things that weren’t even implied, never mind discussed or demonstrated, in the corresponding paper (Quick and Ruben, 2009), could hardly have been all the journalists’ fault.

I was (and still am) angry at such scientists. In my perception, we were at war with anti-science sentiments, and they were playing into the enemy’s hand. Still, it appeared, most of the problem was journalism. Well, this media workshop provided me with a few reality checks. It changed my perspective in some ways, and reinforced my convictions in others. Let me count the ways.

The opening panel in the workshop featured scientists. My first surprise was learning that one of them had absolutely no issue with journalists. He loved making headlines, even if said headlines would make my hair stand on end. He’d found that journalists were generally decent people who want to Get It Right as much as you do.

Then, of course, we got the journalists’ perspective. Their insane work schedules, their pressure to sell stories, their attempt to do so while still retaining accuracy. All in all, they did seem like decent people who wanted to get it right.

But here’s the first problem: given the demands of the job, that can be very difficult to achieve. If, as one of them explained, you might have to report on something even before you’ve had time to actually read the sources, you can very easily make mistakes with the best of intentions.

This is a problem we can help journalists with. Make sure the press office has clear and accurate information so the press release isn’t complete nonsense. When you write a paper, make sure your key points are made clearly and concisely right in the abstract, not in a long and complicated paragraph on page fifteen, where the people writing the news will never see it. If a journalist requests your help, be there to explain and clarify and provide non-wtf quotes. That’s one thing the panellists were very clear about: they need scientists’ cooperation, and they often need it at short notice.

The second problem, I think, is a more fundamental one: scientists and journalists mean something different by “getting it right”. (At least in my idealised world where all scientists think like me. :)) A journalist primarily wants to sell a story, where a scientist primarily wants to increase human knowledge. Of course, scientists also want to sell their stories – no one wants to publish papers that are never cited, and no one wants their career to wither without funding. The crucial difference is, I think, in what each group means by a good news story, and what compromises they are willing to make in order to write one.

For example. To me, direct fossil evidence of how an ancient fish reproduced (Long et al., 2009) is fascinating in itself. I was pretty miffed with the press release accompanying this publication, which turned a relatively mundane finding about the oldest evidence of live birth in vertebrates into a sensational story about the oldest evidence of sex in animals.

If it wasn’t a gigantic digression, I could rant long and hard about all the ways in which this press release mangles science to make it more newsworthy, but the real question is this: does it matter? (To people other than me, I mean.) Is this distortion of facts necessary or even beneficial for getting non-science junkies even a little bit interested? Must we, the scientists, lower our standards of rigour to engage the general public?

Here’s another one. In early 2009, New Scientist ran a controversial feature article about the limitations of the tree of life concept. This article included a discussion of marine ecologist Donald Williamson’s unorthodox hypothesis that the larvae of many animals – which often look very different from their adults and discard most of their baby bodies during metamorphosis – originated from ancient hybridisation events between distantly related critters.

To most people knowledgeable about evolution, genomics or developmental biology, his claims don’t stand up to scrutiny. In our eyes, Williamson is promoting a very implausible hypothesis on weak and superficial evidence. I would only ever bring up his ideas as an example of a “loony theory,” most likely wrong but perhaps interesting from a sociological point of view. But here is a high-profile science magazine, presenting it as an exciting, “different,” and above all, credible alternative to the mainstream view(s) of animal evolution. (In the section on Williamson’s hypothesis, there is no indication of how “fringe” this idea is considered in the scientific community.) The writers at New Scientist were interested in cool stories, and not necessarily in critically examining them.

I see these issues as a fundamental difference between the two professions. I think it’s very difficult to reconcile our demand for accuracy and sound evidence with the journalist’s job. Unlike some audience members at the workshop, I don’t think a formal education in science is necessary to be a good science journalist. Like anything else, a “feel” for science can be picked up by being exposed to lots of it, and scientists are (or should be) there to help out with unfamiliar issues.

However, I do think that we as scientists can’t expect journalists to tell the stories we want them to tell. We can’t expect them not to “dumb things down”, we can’t expect them to respect technical distinctions they don’t see the importance of, and we can’t expect them not to sensationalise a discovery whose true importance is subtle and requires a lot of background knowledge and perhaps a good deal of pre-existing science nerdery to appreciate.

And who knows, maybe the masses reached by sensational news stories are worth a few disillusionments. The angry are always the loudest, and they may not be the majority. I don’t know. But if you are dissatisfied with the way science is represented in the media, griping about journalists to your colleagues isn’t going to solve the problem. This is the age of communication. Anyone can talk to the public. So if you want to change what they hear, why would you wait for others to say the things you want said? Go forth, scientist, and make your voice heard!

***

References:

Quick DE & Ruben JA (2009) Cardio-pulmonary anatomy in theropod dinosaurs: Implications from extant archosaurs. Journal of Morphology 270:1232-1246

Long JA et al. (2009) Devonian arthrodire embryos and the origin of internal fertilization in vertebrates. Nature 457:1124-1127

I has new addiction?

Eduroam is finally letting me play Phylo, a game about aligning DNA sequences. (Woo-hoo! The things that make me happy…) In the game, they are made of coloured blocks, not letters, and there’s an annoying background music you could theoretically turn off but it’s kind of part of the experience. And I can’t. Stop. Playing.

It’s quite interesting, though, in a way.

Things I’ve learnt so far:

1. I have no patience for this shit.

2. Consequently, I suck at DNA sequence alignment.

3. But I’m still better than a computer.

4. Rodents are weird.

It’s a little scary how often and how easily I can beat the computer’s score when I’m not even seriously trying. And there’s not enough excess human brainpower in the world to do all the aligning that needs doing. I suppose the problem is that there isn’t enough computer power either, which is why programmers have to settle for such shitty algorithms in the first place.

I wonder how the same game would look with protein sequences. I guess colour-coding 20 different amino acids would be a little tougher than four bases…

(Hey, idea. Someone should make a game out of Hox gene classification. Wonder if that would solve the problem I spent my undergrad project trying and failing to solve…)

Specialisation is good for your soul

When I was little, I wanted to know everything. At age six or seven, I could whip out an explanation of why the sun shines, nuclear fusion and all, and by the time I hit my teens, I’d memorised the basic properties of a couple of hundred dinosaur genera, everything cetacean, and every planet in the solar system (back when that still included Pluto :-P) My family members are still a bit surprised if a science question comes up over the dinner table and I answer “I don’t know”.

During my undergrad years, specialisation was my nightmare. While I could, I took classes in maths, programming, geology and something vaguely philosophy of science-ish in addition to my compulsory credits in biology. My BSc is called evolutionary biology, but the actual subjects I studied for it range all the way from biochemistry to ecology.

But you know what?

After 2+ years of working on a single part of a single animal, I finally feel like I know something.

As an obsessive learner and insufferable know-it-all, the real world was bound to give me some big shocks. The first was venturing onto the internet, and getting a near-infinite pile of information dumped on me by Google. That experience might have been why I lost most of my interest in dinosaurs – there just seemed to be too much to learn. That’s a hard pill to swallow for a young know-it-all!

And then I went to university, and met the scientific literature. Even more than first googling dinosaurs, that made me realise that I knew nothing. Ever since then, I’ve never quite felt secure about my grasp of any field. There were always papers I hadn’t read, ideas I didn’t really understand, facts I hadn’t included in my reckoning. I often feel like I can’t form an opinion on anything, because there’s a part of a discussion I’ve simply missed or didn’t pay enough attention to.

No, I’m nowhere near satisfied with my current knowledge of my own area (now that I have an area I can call my own). I don’t think I’ll ever be, and if it happens it’s probably a good sign that I should read more. But when I look at my animals, when I have to tell others about my work, I feel… comfortable. This is my stuff, and while I may not know everything, I know some things in an intimate way only close study can give you. It is an immensely satisfying feeling. And it makes me think that perhaps, specialisation isn’t such a bad thing after all.

Macroevolution Airlines

(This post has been mostly written for a long time but I never got round to publishing it. It’s kind of my darling baby, and I never felt quite ready to let it out into the world. Well, every parent has to let go at some point…)

In the creation vs. evolution section of Christian Forums, “macroevolution” is a common topic of name-calling discussion. At some point in what seems like every other thread, a creationist demands “proof” of macroevolution. The common reaction from the evolution side is that the creationist doesn’t understand evolution, and macroevolution is just lots of microevolution, and here is a list of observed speciation events anyway. While the first point is true more often than not, I have been increasingly uncomfortable with the second lately. To my mind, and I think to anyone interested in palaeontology and/or evo-devo, it’s not at all obvious that macroevolution must be fundamentally similar to the everyday adaptations and driftings we commonly observe real-time.

(Image from the UCMP Understanding Evolution site)

What exactly is macroevolution?

Before I continue my musings, I must first clarify what I mean by micro- and macroevolution. I see two interpretations in use in the scientific community, and I don’t think they are entirely equivalent. The “rigorous” interpretation defines microevolution as anything that happens this side of speciation. Populations adapting to short-term environmental change, individuals and their genes migrating back and forth between neighbouring populations, ordinary everyday genetic drift, etc. are microevolutionary phenomena. Macroevolution starts with the formation of new species. The “wishy-washy” interpretation defines macroevolution as “evolution on the large scale”, or “big change”. This is the one I think many palaeontologists would prefer, and many students of evo-devo as well. This is also the one most creationists seem to have in mind. Most – if not all – of the examples in the well-worn speciation lists I’m guilty of pulling out myself are only macroevolution in the first sense. This is something people often seem unaware of: speciation and big change do not go hand in hand.

The definition I prefer (and I changed my mind on this fairly recently) is the second, because despite its vagueness, it gives us a word for something vitally important, all the things that are (usually) bigger than the evolutionary processes we can readily observe on human timescales. How did something resembling a sausage on legs give rise to the mind-boggling diversity of arthropods? How did our own ancestors end up with legs instead of fins? Why did dinosaurs grow into giants and rule the land while the ancestors of mammals retreated to the shadows? This is what macroevolution means to me. As far as I’m concerned, the population geneticists’ kind of macroevolution already has a perfectly good word for it, and that word is speciation.

The question: what is the question?

With that in mind, is macroevolution something different? This is actually at least two questions. One can ask whether the external forces that set out the path of evolution act in the same way on all scales. Did the environment always exert the same kinds of pressures on living things? The answer to this is probably no – from the appearance of oxygen in the atmosphere to the arrival of predators in animal communities, both non-living and living factors have changed the rules of ecosystems many times in earth history. Do the same sorts of pressures that determine the fate of single populations also affect whole lineages? Does selection operate on more than one level? Do the same traits that natural selection favours in ordinary times also help you in extraordinary times? (Another “no”, if David Jablonski can be believed.)

Alternatively, one can also ask whether small and large changes in the properties of organisms are governed by different intrinsic rules. Do, say, new body parts originate through the same kinds of mutations as new hair colours? Are major changes and small adjustments associated with different developmental stages (Arthur, 2008)? Did the nature of variation itself change over evolutionary time (Gould, 1989; Erwin, 2011)? That last one especially intrigues me, and it may yet return in future meanderings. (It’ll return in force if I ever muster the fortitude to discuss the Cambrian explosion ;))

The way to America

In the aforementioned creation vs. evolution debates, physical distance is a commonly used analogy for evolutionary distance. If you believe in centimetres, the argument goes, how can you not believe in kilometres? If you can walk to the kitchen, why can’t you walk a mile?

I think this analogy is worth examining a little further, because it turns out to be great parallel to the micro vs. macro issue. It is true that anyone who can walk can walk a mile. It may take long and it may tire you out, depending on your physique, but it is possible. However, it isn’t very hard to think of destinations that are simply impossible to reach by walking. I live in Europe. Barring ice ages and Bering land bridges, no amount of steps would take me to America. It is still possible for me to go there, but I have to take a flight or perhaps hop on a ship. Is macroevolution like a mile, or is it more like the distance between Europe and the New World? Does a velvet worm-like creature evolve into an arthropod by lots of tiny steps of its chubby legs, or does it take a ride with Macroevolution Airlines?

***

References:

Arthur W (2008) Conflicting hypotheses on the nature of mega-evolution. In: Minelli A & Fusco G (eds.) Evolving Pathways: Key Themes in Evolutionary Developmental Biology. Cambridge University Press, pp. 50-61

Erwin DH (2011) Evolutionary uniformitarianism. Developmental Biology 357:27-34

Gould SJ (1989) Wonderful Life: The Burgess Shale and the Nature of History. W. W. Norton & Co.

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

Men in science

Yet again, the BioEssays editor in chief writes something that reinforces my incipient fangirlhood for him. His latest editorial titled Men in Science raises an important point that I think people concerned about gender equality often forget. Equality goes both ways.

If you read that title you might expect a misguided “what about the menz” screed, but that’s not what it’s about, at least I don’t think it is. Moore suggests that in focusing on the difficulties women in science face, we tend to forget that male stereotypes affect these just as much as female stereotypes do. It’s great to fight for, say, women’s right and ability to be both mothers and scientists, but what about men who wish to be fathers and scientists? Wouldn’t it help both men and women in science if they could take time off for their families without serious consequences (be they material or social)? Plus at the top levels, the people making important decisions are overwhelmingly male, ergo the system can’t really be improved without targeting men.

And this is quite in line with the opinion I’ve come to after a lot of reflection. Women’s equality doesn’t just mean that they are free to become like men. It also means that girly girls are not subtly despised, and neither are girly guys. Because while you make fun of guys’ makeup, while you find it strange that dad would stay home with the kids while mum works her arse off to feed them, what you are doing is putting down traditionally feminine things just like the finest of bigots.

Believe me, that was a difficult perspective for me to accept. I love science and maths, wear more bruises on any given day than I wear makeup in a decade, and want nothing to do with motherhood or the colour pink. Nonetheless, I am the product of a society that expects girls to be girly while belittling them for it. Of course it would be difficult not to laugh at the idea of a perfectly normal guy with painted nails, cooking dinner for his hard-working wife with a toddler tugging at his track bottoms.

Yet if I do, am I not perpetuating the very same prejudices I rebelled against?

Animals, amoebae and plant scientists’ concerns

I recently wondered, in response to an “ideas” paper in BioEssays, whether animals, fungi, slime moulds etc. actually had a multicellular common ancestor. Dickinson and colleagues’ argument (partly) hinged on the shared presence of epithelia, “barrier” cell layers with distinct insides and outsides, in animals and the social amoeba Dictyostelium discoideum. The most recent crop from BioEssays includes a short letter by František Baluška of the botany department at the University of Bonn that challenges this argument.

Plants, Baluška reminds us, also have epithelia. These epithelia are functionally more similar to animals’ than the one Dickinson’s team found in the amoebae. While there may be doubts about amoebae, plants almost certainly became multicellular independently of animals. Ergo, convergent evolution can clearly produce similar tissues in two distant lineages. So why would we take the possession of an epithelium as evidence for a multicellular common ancestor?

Which is a perfectly valid argument, but it misses the point in my opinion.

The botanist writes,

[Plants] evolved their own plant-specific epithelia 3–5, obviously via convergent evolution. This fact alone not only continues to make plausible the traditional independent origin of multicellularity in the metazoa and social amoebae, but it also indicates that the power of convergent evolution should not be underestimated.

Of course it shouldn’t, but Dickinson’s team wasn’t arguing that “the traditional independent origin of multicelluarity” in animals and amoebae was not plausible any more. They find it unlikely that the functional and molecular similarity (does the latter exist between plants and animals?) between animal and amoeba epithelia is convergent, but they are suggesting that we investigate their new hypothesis, not that we summarily throw out the old one. Baluška is attacking a straw man.

Furthermore, he only addresses this one argument, but the thing in the Dickinson article that made me think the most was phylogeny. According to the traditional scenario, it seemed more likely that all those different unikont groups evolved multicellularity independently. But multicellularity is very widespread among unikonts, so precisely what makes the traditional scenario more likely? (Incidentally, has anyone done any actual statistics on this?)

As far as I’m concerned, the letter said nothing to change my mind. Dickinson et al. presented an interesting idea that’s definitely worth a closer look. I don’t think the evidence is currently strong enough to upset the consensus, but the proposal is not at all daft. I have to say I agree that plants should not be ignored, though. Because we can assume that any similarity between them and animals when it comes to being multicellular is the result of convergence, they’d be a wonderful “control group” when people start testing Dickinson et al.‘s hypothesis.

I think that’s something students of evolution should always keep in mind. Plants and animals have little reason to do things in the same way – they diverged very long ago, adapted to completely different lifestyles, etc. If they do so anyway, that might tell us something deeper about the way living things work. A limitation imposed by physics, a very ancient genetic predisposition, or simply the best way to do something – either way, finding the reason will enrich our knowledge of life and evolution. Animal scientists would be well advised to remember that.

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Reference:

Baluška F (2012) Rethinking origins of multicellularity: Convergent evolution of epithelia in plants. BioEssays, available online 26/10/2012, doi: 10.1002/bies.201200134

Animals, amoebae and assumptions

Animals aren’t the only multicellular creatures in their phylogenetic neighbourhood. Social amoebae, many fungi and quite a few of the poorly known choanoflagellates spend at least part of their lives as collections of cooperating cells. Conventional wisdom has been that these groups invented multicellularity independently, but maybe conventional wisdom needs a bit of challenging.

To tell you the truth, I never really thought about the other possibility, that being multicellular is the original state of affair for these organisms. I never really considered the evidence on which the conventional wisdom was based. You could say I didn’t really care either way. A while back I saw a paper that said something about a social amoeba having an epithelium, but I just kind of shrugged and went on with my life. I don’t know, now an article in BioEssays brought this up again, and I’m not sure I was right to ignore it back then. I think Dickinson et al. (2012) have a point, and I think some assumptions may need to be reexamined.

In case you wondered, an epithelium is a type of tissue made of a layer or layers of polarised cells. “Polarised” means that various cellular components – proteins, attachments to neighbouring cells, organelles – are distributed unevenly in the cell, clustered towards one or the other side of the cell layer. Epithelia line pretty much everything in a typical animal’s body, from, well, the entire body, to things like guts and glands. They secrete important stuff like hormones, and their closely packed cells form a barrier to keep molecules and pathogens where they belong. An epithelium was thought to be a uniquely animal thing to have, but looking more closely at that weird little amoeba suggested it may not be.

The paper that I ignored was Dickinson et al. (2011) – yes, by the exact same people who wrote the BioEssays piece. OK, I didn’t completely ignore it. I read enough of it to scribble a quick note in my citation manager saying “screams convergent evolution to me”. The paper examined the multicellular stage in the life of Dictyostelium discoideum, an ordinarily single-celled amoeba that reacts to food shortages by crowding together with friends and family to form a fruiting body that helps disperse some of its cells in search of new habitats. The fruiting body is pretty complex for a “unicellular” creature, and it turns out that this complexity includes a region of tissue that looks quite a lot like a simple epithelium. It doesn’t just look like one; it sorts out its insides and outsides with the help of proteins called catenins, which are also involved in cell polarity in the epithelia of animals. (Below: D. discoideum being multicellular, from Wikipedia)

That isn’t much evidence to base an inference of homology on, especially since other key players in animal cell polarity are entirely absent from D. discoideum. But equally, the fact that tons of unikonts (the group including amoebae, slime moulds, fungi, choanoflagellates and animals) are single-celled doesn’t mean that the multicellular groups all came up with the idea independently. Evolution doesn’t always increase complexity – sometimes complexity becomes superfluous.

I remember when we discussed the choanoflagellate genome paper (King et al., 2008) in class. The genome in question belongs to a purportedly single-celled creature, but it contains tons of genes you’d think only multicellular organisms would need, such as genes for cell-to-cell adhesion proteins. So one explanation is that these proteins originally did something else, like anchoring a single cell to its favourite spot. Another explanation is that they did have something to do with multicellularity – it just wasn’t the multicellularity of animals at first.

This suggestion isn’t terribly controversial when you’re talking about choanoflagellates, since some of them do obviously form colonies (one such colony of Salpingoeca/Proterospongia rosetta is shown below, from Mark Dayel of the King lab via ChoanoWiki). It’s not hard to imagine that either the “single-celled” species whose genome was sequenced also has a colonial stage the scientists just never saw, or that its recent ancestors did.

Whether or not the same applies to the whole of unikonts is a more difficult question. I’m not at all familiar with the details of unikont relationships, but based on the tree shown in the BioEssays article, multicellularity is all over the group. In most cases, it’s facultative multicellularity; animals are rather the exception in being doomed to it for their entire lives. However, if you just looked at that tree, you’d wonder why the hell anyone thought the common ancestor of these things wasn’t some kind of multicellular.

Yet the details of animal-like multicellularity aren’t so widespread. True cadherins (the cell adhesion proteins I mentioned) have only been found in animals proper. Choanoflagellates and some even more obscure relatives of animals have bits and pieces of them, and other unikonts have none at all as far as anyone knows. Epithelium-like tissues have only been described in that one species of amoeba – but, as Dickinson and colleagues note, no one really looked in the others.

Personally, I wouldn’t be at all surprised if the conventional wisdom ended up shifting. I still don’t think that the evidence from Dictyostelium is enough to draw a conclusion. We obviously need to know a lot more about unikont genomes, tissues and life cycles to piece together the history of multicellularity in the group, but I’m not sure that right now a unicellular ancestor has a lot more going in its favour than a multicellular one. Guess we’ll have to wait and look with an open mind 🙂

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References

Dickinson DJ et al. (2011) A polarized epithelium organized by β- and α-catenin predates cadherin and metazoan origins. Science 331:1336-1339

Dickinson DJ et al. (2012) An epithelial tissue in Dictyostelium challenges the traditional origin of metazoan multicellularity. BioEssays advance online publication, 29/08/2012, doi:10.1002/bies.201100187

King N et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783-788

 

The right amount of pedantry

This is a questions I’ve been wondering about ever since I first attempted to communicate with people who didn’t know all the stuff I did.

Just how pedantic should I be? Just how much scientific accuracy is it OK to sacrifice for the sake of readability?

I am a pedant by nature. Chalk it up to Asperger’s if you like, but when I write about anything remotely technical, I take the utmost care not to give misleading impressions or misuse terminology. For instance, I’ll guarantee you you will never see me use “genetic code” to mean anything other than this (source: Wikipedia):

The genetic code is the set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells.

The code defines how sequences of three nucleotides, called codons, specify which amino acid will be added next during protein synthesis.

The genetic code is not “information in DNA”, “DNA sequence”, or whatever other vague concept journalists like to apply it to. I get disproportionately pissed if I see it misused. Likewise, I’ll tie myself in knots rather than blur the distinction between a gene and its gene product. A Hox gene doesn’t regulate other genes, the resulting Hox protein does; and a homeobox encodes, not is, a homeodomain. If I dug through my forum and blog posts, I could list many more examples of my absolutely anal attitude towards terminology.

Am I overdoing it? It’s a good bet most people who might stumble on this blog are not molecular biologists, and I’m as sure as sure can be that my creationist “audience” over at Christian Forums wouldn’t know what a gene was if it came with an info board like animals in the zoo. By making these technical distinctions, am I just causing more confusion? Am I turning off potential readers? Is it better for me as a science communicator to go the journalist route and not give a shit whether I was talking about a gene, or the protein – or RNA* – it contains the instructions for?

(And – would I hate myself for it?)

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*See, I just had to add that. Because not all genes encode proteins, and somehow that matters in a post that has nothing to do with genes. If you didn’t know what I was talking about, this footnote is pretty much it.