Category Archives: Evolution

‘Ferns have not bowed to the ages’

When I started my undergrad, botany was something of an afterthought – I just needed a third course to go along with chemistry and zoology, which had been my mainstays in A Levels. But once I sat down in Dr Duncan’s class, I was enthralled – while chemistry and zoology largely rehashed what I had learned in A Levels, botany took me into an entirely new world. As we partook in an old-fashioned march across the plant kingdom, I was amazed. Lectures were interesting, but it was the labs that truly drew me in.

By the time we got to ferns, we had covered a variety of algae and simpler plants. Much of what I was taught slipped past me, adrift without a proper foundation. The difference between isotomous and dichotomous branching in the thallus. Steles, and steles within steles. But one thing that stuck with me was a quote from Frederick Orphen Bower: ferns, he said, had not bowed to the ages. While other ancient groups like the liverworts and horsetails had retained only a shadow of their former diversity, ferns were not only diverse, much of their diversity reflected a (relatively) recent diversification that had occurred ‘in the shadow of angiosperms‘.

The simple fact that ferns diversified after the rise of the group that is generally seen as replacing and displacing them is in itself remarkable. It clashes, not with evolutionary theory, but rather, with our (mistaken) perception of an orderly progression of evolution. If we can put aside our evolutionary misconceptions, it becomes less disconcerting. Or it did, until recently.

A recent paper by Fay-Wei Li and colleagues uncovers the mechanism by which ferns were able to diversify in the shadows: a gene from a hornwort. In is usual way, Ed Yong does an great job of explaining the research, as does Carl Zimmer. While the discovery is a great story, what really intrigues me is the mechanism of gene transfer. Horizontal gene transfer (i.e., transfer from one species to another) is no big deal in bacteria. Migration of genes from the mitochondrial and chromosome genome to the nuclear genome is strange, but it’s still the kind of thing for which you can envision a reasonable mechanism. Gene flow between species via introgression (hybridisation followed by extensive backcrossing to one parental species) is intuitive (or can be, if you don’t think about it too much). But transfer of a gene from a hornwort to a fern. How is that supposed to happen?

As odd as it sounds, I’m sure there’s a reasonable way for genes to make that journey. I’ve heard about people coaxing plants to take up RNA molecules. Viruses could also have unwittingly played a part. I suppose the most important message in this story may be the realisation that transgenic higher plants may not be as unusual as we tend to think they are.

Speciose or species-rich?

[Repost from my old blog]
As a graduate student I came across the word “speciose”.  It had an alluring sound to it that was lacking in its more pedestrian synonym “species-rich”.  Equally appealing, I suspect, was the fact that it supplied a formal-sounding alternative that was less accessible to the average person.  (If you’re lucky, you outgrow that affectation and learn that clear communication is what matters most.)

In the December 2008 issue of TREEMichael Hart delves into the origin and use of the word speciose.  Although similar to “species”, speciose actually shares a root derives from “specious” in ‘beautiful’ or ‘lovely’.  Hart sees value in speciose – it’s no longer than “species-rich” and solves the hyphenation problem (i.e., the problem of not knowing when to join the words “species” and “rich” with a hyphen).  Both “species-rich” and “speciose” first show up in the Web of Knowledge database in 1957, and use of both terms has grown fairly consistently.  Although he cites Gill’s plea to cease ‘the misuse of ‘‘speciose’’ in the evolutionary biological literature,’ Hart sees value in this “lovely word” and urges “deliberate consideration” as to its future and fate.

I embraced “speciose” in my first or second year as a grad student.  I happily embraced it, using it both in writing and conversation.  And then, to my horror, I discovered Gill or some other pedant who insisted that “speciose” was being misused by ecologists.  With that discovery, I banished the word from my vocabulary.  The only thing worse than using big words is misusing them.  Granted, it had been wearing thin already – my doctoral advisor, for example, had seen no inclination to adopt the word despite my repeated use of it.

And that’s where it’s stood for me, until now.  Al Gentry used to word, and being as amazing a biologist as he was, he had the right to use whatever word he wanted, however he wanted to…and be right.  He was, after all Al Gentry.  (And he had tragically passed away, doing a rapid assessment of biodiversity.) Reading Hart made me re-think my opposition to “speciose”.  We have the right to re-define words from time to time, and this might be a good candidate.  I’m not sure if it’s for me (it’s been four years since I wrote this post and I have not started using it), but I should be willing to consider it an acceptable term.

Hart, Michael W. 2008. Speciose versus species-rich. Trends in Ecology & Evolution,23 (12):660-661 doi:10.1016/j.tree.2008.09.001

What do evolutionary biologists study?

So what do evolutionary biologists study? Evolution is, in the minds of much of the public, ‘controversial”. In no small part, this is the doing of a large, vocal, well-funded anti-evolution movement. But responsibility also lies with the people who have taught evolution, who work in the field of evolution.

A lot of people see evolution as being pretty much the same as palaeontology. People dig up fossils and then come up with explanations for how these fossils are related. One person calls a certain fossil a human ancestor. Another says that is represents a distinct lineage. From the outside it just looks like a group of people with advanced degrees pontificating about a subject…specifically, the subject of origins. To look at it another way, it it seems rather a group of scholars discussing some esoteric element of theology.

If I’m correct, that might explain a good deal of how American (especially evangelicals) see evolution. To American Protestants, theology and christology tend to be a very personal endeavours. The Protestant Reformation led to the translation of the Bible into the tongues of the common people. Not only were they able to read the words for themselves, they were also encouraged to come to their own conclusions about it. Looking in from the outside, it’s easy to see evangelical and fundamentalist churches telling their members what they should believe about a number of important issues. But most churches also tell people that they should find their own meaning in scripture. If you aren’t willing to take your own pastor’s word on the meaning of everything in the Bible, why should you take the word of some ivory-tower intellectual who (a) almost certainly knows nothing of the life experience of people like you, (b) is just one voice among many, each of whom has a different view of what this fossil means, and (c) is probably an atheist with an agenda to undermine Christianity and morality.

Now, obviously, this approach is entirely incorrect. Science isn’t a collection of equally valid ideas – some ideas are demonstrably better than others, while others are demonstrably worse. The diversity of views that anti-evolutionists speak of, just doesn’t exist. More importantly, there is no hierarchy imposing orthodoxy.

But more people don’t understand this. And sometimes, I suspect, evolution defenders miss this point entirely. [More later]

Opening reception

For most people, Evolution 2011 got off to a start tonight with the opening reception at the Sam Noble Oklahoma Museum of Natural History (SNOMNH).* Upon arrival, we met long registration lines which threatened to spill out the building into the 100°F (38°C) outdoors. Luckily, since we had registered early, we were directed past the lines directly into the main hall. It’s a familiar space where I’ve attended many receptions and seen many distinguished speakers. In his portion of the welcome address, College of Arts and Sciences Dean, Paul Bell, reminisced about the opening of the museum 11 years ago, when Stephen Jay Gould stood and spoke on the very spot where Bell was now speaking. Bell raised an issue that came up many times in conversation tonight – the importance of science education and the embattled status of evolution in the state of Oklahoma today.

It is, of course a very valid concern. Several anti-evolution bills lost or died in committee this session through the hard work of groups like the Oklahomans for Excellence in Science Education. Sure, there’s a religious and political basis for much of the hostility to evolution in Oklahoma, but there’s also an element of ignorance as to what evolutionary biology is. What, someone asked, do evolutionary biologists do? This isn’t really an evolution-specific question. Few members of the general public could answer what any specific sub-field of knowledge actually studies. But creationists have done a good job of exploiting this particular hole in ‘common knowledge’. All evolution does is look at fossils and guess at how the fossils evolved, right? And it’s not really a science because you can’t do any experiments. A little ignorance, reinforced by a few creationist memes, and suddenly people “know” that evolution is not a science. So why are all these people here in Oklahoma – to engage in socialist plots against God-fearing Americans?

The real answer, of course, is fairly easy to find. But would the public be able to deduce anything from it? The first set of talks, spread across eight concurrent sessions include

  • Introduction to models of character state-dependent diversification
  • Variable environments, fluctuating selection and the stability of breeding partnerships in birds
  • Rapid adaptation to anthropogenic environments via hybridization?: Invasive hybrid watermilfoil genotypes are more common than parental genotypes in herbicide-treated lakes
  • Wedge effects: the shape of dispersal barriers and spatial population genetics
  • The evolutionary tale of the largest C4 eudicot lineage: North American desert origin, highly reticulated evolution and extraordinary Hawaiian Island radiation in the Chamaesyce clade of Euphorbia (Euphorbiaceae)
  • The genetic architecture of a difference in male genital morphology between Drosophila mauritiana and D. sechellia
  • Evidence of a resident species of Plasmodium in the Galapagos avifauna
  • Evolutionary genomics of biofilm adaptation and diversification

While I’m sure the average person might have a hard time figuring out what the practical applications of any of this might be, a few things are evidence – no dinosaurs, no fossils.

I find myself wondering – would that really help? Would the public be any more positively inclined to the study of evolution if you could show them that it’s not just a group of people trying to disprove the existence of God.Or would the conversation simply switch to “wasteful spending”?

The opening reception was pretty good. I met Carl Zimmer, one of the best science writers out there. Wine and beer were available at the reception, but only with a drink ticket. Since there were only spaces for tonight, attendees were limited to two alcoholic drinks. I’m sure there are a lot of good reasons, but when I jokingly said something about it to one of the people behind the bar, he replied “well it is a museum”. That led to a rather hilarious image of crowds of drunken evolutionary biologists rampaging through the museum and reclassifying things based on rival phylogenetic hypotheses.

*Try saying S-N-O-M-N-H. The first challenge is the difficulty in remembering the acronym. Usually it works the other way – you remember AMNH, and use that to remind yourself ‘American Museum of Natural History’. Here though, you need to remember “Sam Noble Museum of Natural History”, and cross-check that with the sequence of letters that’s coming out of your mouth. Already, mnemonic fail. But there’s also the sequence of letters. Sure, AMNH has the same sequence, but with only four letters you say each one separately. Here though, you end up with words; ess’no em’naitch. Funny-sounding words.

Evolution 2011

The 2011 Evolution meetings are in town. Four days of scientific presentations on evolutionary biology, a field whose very existence many creationists would cast into doubt. Today was just the initial things – arrival, registrations, and workshops for K-12 teachers in Oklahoma. I headed over in the late morning, registered, and perused the (only partially set-up) displays by merchants. It is, I have learned, an important part of meetings. I love all things book-related, so browsing books and journals and chatting with publishers reps are fun.

Next up – the opening reception at the Sam Noble Oklahoma Museum of Natural History. I was planning to walk over there – it’s about a 20-minute walk, and at 7 pm it should have cooled down enough to make for a pleasant walk. Which just goes to show that I still don’t understand Oklahoma weather. At 7 pm it’s still 100°F (38°C). Granted, that’s down from 104°F (40°C), but it’s still ridiculously warm. And while I still expect the sun to set by 6 pm, it does nothing of the sort in Oklahoma in summer.

The conference proceedings look interesting. It’s not an ESA or ATBC meeting, but a lot of it is still within my general area of interest (and some isn’t. I don’t care about tools for building phylogenies, even if I do care about phylogenies – I’m a consumer of systematics, not a producer.) Anyway, scientific meetings are fun, any way you put it…