A bit of Hox gene nostalgia

I had the most random epiphany over my morning tea today. I don’t even know what got me thinking about the Cambrian explosion (as if I needed a reason…). Might have been remembering something from the Euro Evo Devo conference I recently went to. (I kind of wanted to post about that, because I saw some awesome things, but too much effort. My brain isn’t very cooperative these days.)

Anyway.

I was thinking about explanations of the Cambrian explosion and remembering how the relevant chapter in The Book of Life (otherwise known as the book that made me an evolutionary biologist)  tried to make it all about Hox genes. It’s an incredibly simplistic idea, and almost certainly wrong given what we now know about the history of Hox genes (and animals)*. At the time, and for a long time afterwards, I really wanted it to be true because it appeals to my particular biases. But I digress.

Then it dawned on me just how new and shiny Hox genes were when this book was written. I thought, holy shit, TBoL is old. And how far evo-devo as a field has come since!

The Book of Life was first published in 1993. That is less than a decade after the discovery of the homeobox in fruit fly genes that controlled the identity of segments (McGinnis et al., 1984; Scott and Weiner, 1984), and the finding that homeoboxes were shared by very distantly related animals (Carrasco et al., 1984). It was only four years after the recognition that fly and vertebrate Hox genes are activated in the same order along the body axis (Graham et al., 1989; Duboule and Dollé, 1989).

This was a HUGE discovery. Nowadays, we’re used to the idea that many if not most of the genes and gene networks animals use to direct embryonic development are very ancient, but before the discovery of Hox genes and their clusters and their neatly ordered expression patterns, this was not at all obvious. What were the implications of these amazing, deep connections for the evolution of animal form? It’s not surprising that Hox genes would be co-opted to explain animal evolution’s greatest mysteries.

It also occurred to me that 1993 is the year of the zootype paper (Slack et al., 1993). Slack et al. reads like a first peek into a brave new world with limitless possibilities. They first note the similarity of Hox gene expression throughout much of the animal kingdom, then propose that this expression pattern (their “zootype”) should be the definition of an animal. After that, they speculate that just as the pattern of Hox genes could define animals, the patterns of genes controlled by Hoxes could define subgroups within animals. Imagine, they say, if we could solve all those tough questions in animal phylogeny by looking at gene expression.

As always, things turned out More Complicated, what with broken and lost Hox clusters and all the other weird shit developmental “master” genes get up to… but it was nice to look back at the bright and simple childhood of my field.

(And my bright and simple childhood. I read The Book of Life in 1998 or 1999, not entirely sure, and in between Backstreet Boys fandom, exchanging several bookfuls of letters with my BFF and making heart-shaped eyes at long-haired guitar-playing teenage boys, I somehow found true, eternal, nerdy love. *nostalgic sigh*)

***

*Caveat: it’s been years since I last re-read the book, and my copy is currently about 2500 km from me, so the discussion of the Cambrian explosion might be more nuanced than I remember. Also, my copy is the second edition, so I’m only assuming that the Hox gene thing is there in the original.

***

References:

Carrasco AE et al. (1984) Cloning of an X. laevis gene expressed during early embryogenesis coding for a peptide region homologous to Drosophila homeotic genes. Cell 37:409-414

Duboule D & Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. The EMBO Journal 8:1497-1505

Graham A et al. (1989) The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57:367-378

McGinnis W et al. (1984) A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes. Nature 308:428-433

Scott MP & Weiner AJ (1984) Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. PNAS 81:4115-4119

Slack JMW et al. (1993) The zootype and the phylotypic stage. Nature 361:490-492

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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…

 

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

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.

The small joys in life

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

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

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

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

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

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

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

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

*Crack*

My heart is a bit broken.

On my way to work this morning, I saw a crow tearing into the corpse of a small bird, possibly a greenfinch from the brief look I got. I don’t know if the crow had killed it or if it had dropped dead all by itself, but in the end it doesn’t really matter.

I love crows and I know they are opportunistic bastards that will eat anything, but I’ve never actually seen one feast on a small bird. And small birds are my little feathered antidepressants. It’s like seeing your beloved cat dismember your pet hamster.

I’ll console myself with Andreas Trepte’s gorgeous photos of a non-dismembered greenfinch. Isn’t he a beauty!

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?