Someone has probably already done this, but still.

Image stolen from the interwebs, inspiration found in The Ancestor’s Tale.

mass extinctions, biology, kanye west

Reading The Ancestor’s Tale.

I have now learned sometihng so shocking that I am still reluctant to beliee it, but it looks as though I am going to have to. Hippos’ closest relatives are whales. The even-toed ungulates include whales!

This makes me think. I was not whatsoever surprised to learn this. And certainly not shocked. I wonder when the day will come that a cladistic revolution like this one will actually stir me into a deeper reaction than “Oh? That’s interesting!”. And I wonder what’s preferable? Being so open to new thoughts, new evidence, that nothing shocks you? Or getting a little more set in your thinking, so that your world might actually be fundamentally shaken occasionally, as science progresses?

I wonder if it’s a generational thing; maybe people my age are so used to the world ever-changing, having seen technology like mobile phones and the internet evolve from bulky simplicity to exquisite complexity as we were struggling through puberty, that we’re unable to even feign surprise. Or maybe I will eventually grow up. Maybe the next time the tree of life sees a significant change I will be shocked.

Time will tell.

evolution, biology, science

The latest Carnival of Evolution is out (and would you believe I just almost spelled that “evilution”?)! It’s in two parts and full of great posts on many different aspects of evolution.

Go check it out!

Part #1, Part #2

evolution, biology, blog carnival

Here’s me grudgingly getting on the bandwagon and helping in the dissemination of the Tree of Life video with David Attenborough.

It’s very pretty. And all the facts are correct, so far as I’m aware. But this video still makes my skin crawl a bit. Why? Because it’s pretty much a perfect illustration of one of the problems I discussed in my post on tree thinking. Here’s evolution depicted as a linear process, with a clear line of progression from the simplest forms of life towards … well, humans, of course. What else?

They do mention insects invading land long before vertebrates did, which is nice. And there’s a short digression into dinosaur territory. But still - the video essentially supports a view of life where evolution inexorably works towards its goal, which is apparently primates with large brains. A tiny group of animals on an earth veritably crawling with other much more abundant forms of life. A self-centered, egotistical species, who cannot for a moment let go of the idea that we’re the pinnacle of creation, whether that creation was effected by a god or physical processes.

Also the video fails to point out that mammals came from the very same lineage Attenborough claims is ancestral to today’s tortoises, snakes, lizards, crocodiles and dinosaurs (including birds). It’s like mammals simply turn up by magic and start taking over the earth once the dinosaurs are gone.

And of course, there’s the glaring omission of the huge part of the tree of life that’s not animal. Plants and fungi are pretty much entirely ignored, bacteria are mentioned briefly and archaea not at all. This is ok, of course - the study of animals is obviously bound to be extra interesting to animals capable of appreciating said study - but I find it disingenious to call it a study of the tree of life when in fact we’re just looking at one of the several main branches.

But. It feels wrong to be critical of Attenborough. He has probably done more to popularise biology than anyone, and although he’s not a scientist he usually gets his facts straight (which, lately, feels more like a boon than it should) - so who am I to complain? Here’s a couple of things I really like about the video:

Firstly, Attenborough states that life began 3000 million years ago, rather than 3 billion. This is a very nice rhetorical trick to make people start realising just how vast a span of time we’re talking about. Graphically, the fact that the tips of the branches are all at the same level somewhat counteracts the idea that any living species is at the “top” of the tree. All living species are! Finally, the video does end with Attenborough pointing out that we mammals actually share the world with many other lineages.

So, Sir Attenborough, should you by any chance read this - I still love you. Just don’t do it again, ok? Now go to your room.

attenborough, tree of life, biology, evolution

Dear Britain: What the fuck?

Half of British adults do not believe in evolution, with at least 22% preferring the theories of creationism or intelligent design to explain how the world came about, according to a survey.

My first reaction upon reading this was: Kudos to the British public! Evolution does NOT explain how the world came about. Creationism actually does that better, since evolution doesn’t even attempt it. If the survey actually asked them if evolution explains “how the world came about”, no wonder the results were abysmal.

Now, the question is, was the survey really as stupid as the Guardian makes it out to be? This press release from Theos Think Tank seems to dispel that notion. It’s simply the case that the journalists and editors at the Guardian has gotten their heads stuck up their asses. Unfortunately, so do the people at Svenska Dagbladet, a Swedish newspaper that picked up the item and pretty much translated the article from the Guardian.

Why, journalists? Why must you make my job so difficult before I’ve even got one? I’m very nearly contemplating giving up my career plans as a biologist to become a science journalist intstead. At least I’d be halfway competent.

(And no, I’m not even touching the fact that the British public is in sore need of some good science education. With newspapers like the Guardian around to confuse people, I’d say the figures cited are pretty good.)

Hat tip to Terra Incognita and commenters.

ETA: Bob Churchill sets things right. Dear gods, the whole thing’s a mess when you think about it.

evolution, uk, science, journalism, science journalism

Since a few years back, Sveriges Ornitologiska Förening (Swedish ornithological association) has been involving the public in a great bird-counting exercise every January. Between dawn on a friday and dusk the monday after, we’re encouraged to keep track of what birds visit our bird feeders. More specifically we’re supposed to report the greatest number of each species observed at once. The resulting data is used to track fluctuations in bird populations all over Sweden.

It’s a fantastic way to involve the general public in scientific endeavours. The only thing I could wish for is that they’d push that side of things a little more - make people aware that that’s what they’re doing. Sure, the data is perhaps not as rigorous as would be required to publish in a scientific journal, but it’s definitely good enough for tracking changes and getting some idea of what’s going on.

Anyway, naturally me and my parents were keeping unusually close tabs on our own little feeding station over the weekend. This year our count was:

Great tit: >20. Probably at least 25. It’s very difficult to count when there’s that many!
Blue tit: 6. For a long time we spotted no more than two or three at the same time. Then we supplied an extra ball of fat (I have yet to find out what this might be called in English - it might be a scandinavian phenomenon. Looks like this.) and that brought them out of hiding.
Coal tit: 3. There might have been one or two more but we rarely see many of these at the same time.
Marsh tit: 2. Conspicuously absent most of the time. Marsh tit are normally regulars.
Yellowhammer: 2. And only for a brief time. We don’t supply oats so we’re probably not their favourite feeder.
Great spotted woodpecker: 1. Liked the peanuts but avoided the pig fat, oddly enough.
Nuthatch: 2.
Blackbird: 6. Mostly active at the crack of dawn when the other birds are barely awake. Likes apples.
Long-tailed tit: 6. Was so stoked to see a group of these absolutely adorable little tits on sunday. You know how some people go all gaga over cute puppies? That’s me with long-tailed tits. I start squeaking baby-talk for a few minutes.

These are pretty low figures and above all there’s several species missing. Where’s our friend the crested tit? Where are the jays? And what about the greenfinches and chaffinches? And my personal favourite the treecreeper? Part of the explanation is probably that weather has been pretty abysmal - above all it’s been too warm. When there’s no snow on the ground, the birds don’t particularly need the feeder. Many of them still show up, but nowhere near the great variety we see when it’s cold and snowy.

birds, bird feeding, ornithology

Darwin’s first tree

The following post is a crash course in how to interpret evolutionary trees written for the layman. I’ve avoided all the tricky nomenclature (like “phylogeny” and “cladogram”) for clarity. Enjoy!

As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.
-Charles Darwin

When Darwin presented his theory on the origin of species by means of natural selection, he chose to illustrate the evolution of lineages by means of a tree. It’s a metaphor and a method that has stayed with us since then - for better or for worse. These days, we know that what evolution has produced is more of a sprawling shrub with mostly dead branches, rather than the majestic tree Darwin envisioned, and that the base of the shrub is probably more like a web than a trunk. (As most of you are no doubt aware by now, New Scientist recently had a story on this with a frightfully dumb headline on the cover.) These issues aside, depicting the relationship between species by the use of trees has turned out to be immensely useful.

Evolutionary trees are now ubiquitous; apart from being all over the scientific literature, they also turn up in museum exhibits, newspaper articles and wherever else the relationships of different species are discussed. Trees are a powerful and intuitive graphical representation of evolutionary relationships - but there are pitfalls. There is still a lot of confusion among people in general (and even biologists) when it comes to how these trees should be interpreted. We all have a tendency to read things and interpret images a certain way, and we often imagine an order of progression even when the data doesn’t support it. Many biologists don’t realise how important it is to choose a graphical representation of their data that isn’t just correct, but also doesn’t trick the viewer into believing conclusions that simply aren’t there; conclusions that have nothing to do with biology.

The ape branch

Case in point, take a look at the tree to the left. Humans are clearly at the top of this tree. It supports the idea that we are the pinnacle of evolution, the end result, perhaps even the reason for it all, don’t you think? No. In fact, the tree says that humans are entrenched among the apes, as much a primate as any of them. But since a lot of people haven’t learned “tree thinking”, that’s not what a lot of people see.

Because (at least in the west) we read from left to right, the tree depicted implies an order of progression from gibbons to humans. Some people would go so far as to interpret this tree as saying that gibbons evolved into orangutans, which evolved into gorillas, which evolved into chimps, which finally evolved into humans - the age-old “If humans came from monkeys, why are there still monkeys?” fallacy.

Gratuitous platypus

Even if you don’t fall into the progression trap, the tree still suggests at a glance that gibbons are more “primitive” than the rest. And this fallacy is something that’s not restricted to laymen. Some biologists would refer to the gibbon branch as “basal”, and it’s quite common to talk about “higher” and “lower” forms of life. This is all poor tree thinking. As long as all the species depicted in the tree are alive today, and as long as the assumption is made that life only begun once on earth, it’s important to remember that every single extant lineage has evolved for exactly the same amount of time. The “lowliest” of bacteria have been evolving for the same amount of time as us humans. We may say that some forms of life possess more “primitive characters” than others. For instance, monotremes are mammals that lay eggs, and since we believe that the ancestors of all mammals also laid eggs, we may call this a primitive trait - but that doesn’t mean that the monotremes are in some way less evolved than the rest of the mammals. They simply possess fewer derived traits.

So what can we say about this tree? What it tells us is that humans and chimps share a common ancestor that is more recent than the ancestor of humans, chimps and gorillas. The hypothetical ancestors are represented by the nodes of the tree. Conversely, it tells us that the lineage that would eventually become gibbons split from the rest earlier than the lineage leading to orangutans. It doesn’t say anything about what the hypothetical ancestors were - this tree in no way implies that the common ancestor of humans and chimps looked more like a human or a chimp. All we know is that it shared some traits with the lineage that led to the gorillas, which implies - to us, although the chimps might disagree - that that ancestor might have been more like the other apes than a human. Had the other apes been omitted from this tree and replaced by a fish, it would have been anyone’s guess as to whether chimps or humans possessed the most derived traits.

Finally I’d like to mention the concept of relatedness. When looking at a tree, how can you tell which species are more closely related to another? Firstly I would actually be wary of using the term “related” in this case at all. Rather than saying “this species is more related to that species than the third one”, I would say “these two species share a more recent common ancestor with each other than with this third one”. Because common ancestry is what this is all about. It is easy to look at a tree like the one above and get the idea that orangutans are more closely related to gibbons than to humans - they are adjacent to each other and only one node separates them. This is not correct. The common ancestor of orangutans and humans is more recent than the one of orangutans and gibbons, which means that orangutans and humans are more closely related.

Wrapping up, I present a very simple exercise for the reader! After reading this post you should be able to answer the following questions no problem, and as a little perk, the people who give me three correct answers will get to give me a topic or question of their choice to blog about (anything you like within reason - the more interested I am in the topic the better the post will be - if you ask me about the political situation in Nepal, or anywhere really, I’m afraid I’m stumped).

1. Are the trees below identical? (If not, how are they different?)
2. “In the first tree, species L is more closely related to species S than P.” True or false?
3. “In all trees, S, C and L share a common ancestor.” True or false?

biology, evolutionary trees, evolution, phylogenetics

Like John Whitfield at Blogging the Origin, I’m taking the opportunity to read Darwin’s On the Origin of Species now that it’s been 150 years since its publication, and 200 years since its author’s birth. I figure if I’m ever going to read it, now is the time. Unfortunately I’m not quite as fast as John, which means I’m not actually reading his blog, as I don’t want any spoilers.

Well, ok, I already know the book’s conclusion. But I want to experience each chapter without preconcieved notions and hence I’m putting off reading John’s comments until I’ve finished them myself … and I have yet to finish the first chapter. A few pages before going to sleep each night is the pace I’ve set.

Since I’ve only just started I don’t have much to say, except that so far, I’ve quite liked it. Apart from his incessant abuse of commas (which I know is simply indicative of when it was written), Darwin’s a good author. I don’t see why people complain about the pigeons in the first chapter - I think it’s brilliant. Darwin knows he’s going to upset a lot of people with his ideas, and so he starts out with the deviously innocent topic of breeding pigeons. It’s fantastic.

What’s also fantastic is how he keeps touching on areas where I, as a mere biology student in the 21st century, could totally fill him in. Although he was, to my knowledge, unfamiliar with Mendel’s ideas on inheritance at the time, he still seems very close to the right idea, occasionally. Perhaps, if his brain hadn’t already been so chock full of all that knowledge, he’d have had the intellectual energy to do some experiments and put things together. As it is, he didn’t, and maybe that’s a good thing. Maybe, the world needed that time of uncertainty to adjust, before the modern synthesis happened.

Anyway, I must say it’s a lot easier to read than I thought it would be. I’ve read most of Voyage of the Beagle already, and thought the Origin would be heavier, but it isn’t.

Expect more posts on the On the Origin!

darwin, origin of species, evolution

So, been a bit of a hectic week. The course in Molecular Ecology I mentioned finished on friday, meaning I spent the days prior to that frantically trying to finish the paper and presentation of the final project. It was on butterflies.

…

Oh alright. Here’s part of the introduction (the only interesting part of the paper, in my opinion):

The mating behaviour and associated pheromones of pierid butterflies, among them the green-veined white butterfly P. napi, have been studied extensively by Andersson et al. (2000, 2003 & 2004). These butterflies are polygamous, with males seeking out and courting females, which may then allow or refuse copulation.

During copulation, the male P. napi transfers a spermatphore to the female’s bursa copulatrix. This packet contains not only sperm, but also nutrients and pheromones, and is quite large – the mass can extend to 23 % of the female’s body weight. Recently mated females hence cannot receive another packet until they have absorbed the old one (Forsberg & Wiklund, 1989). Also, both mating and oviposition must take place during fair weather, which restricts the time a female can spend on both activities. Thus, females should be allocating more time for oviposition than mating when they are recently mated. This is facilitated by an anti-aphrodisiac transferred to the female during mating. The anti-aphrodisiac, methyl salicylate, is synthesised only by males.

When approached by a male, the female adopts a so called “mate-refusal posture”: She spreads her wings and lifts her abdomen. This posture is well suited for spreading pheromones from her abdomen, while at the same time preventing the male from copulating with her. Females initially adopt this posture regardless of whether they are receptive to mating or not. Receptive females will however, after having been courted by the male, lower their abdomen so that copulation may ensue. Males will approach any female, but quickly abandons recently mated and thus unreceptive ones – it appears that males are incapable of forcing females to accept their spermatophores, and hence they have no incentive to court an unreceptive female.

Females who have received methyl salicylate are thus less likely to suffer extended harassment from unwanted suitors, and can spend more time laying eggs. This also benefits the male, as it maximises the amount of his sperm that is used before an eventual remating. This is an interesting example of how sexual selection may sometimes lead to co-operation between sexes, rather than sexual conflict.

Stand back - I’m going to try science.

Thrilling, isn’t it? Our study, conducted over the course of about ten days, was quite simple. Our task was to find out whether males can utilise three different compounds to synthesise the anti-aphrodisiac. In the picture I’m posing with a gas chromatographer coupled to a mass spectrometer, used to identify volatiles emitted by male butterflies.

Oh you wanted to know the results? They could use two of the compounds we tested but not the third. That’s pretty much it.

Yeah, this is not my subject. The other two groups had more fun projects - paternity analysis in arctic foxes and phylogeography of … some other butterflies. They got to work with DNA! I was intensely jealous, but at least now it’s over. (And I got a B on the course. This corresponds to 85-95% correct marks on an exam so I’m quite happy.) Also, the next course I’m taking, which begun yesterday, is Molecular Systematics. So it’s pretty much guaranteed to be fun.

biology, science, pheromones, butterflies

There must be something wrong with the link between my science gland and the pleasure centre of my brain. I mean, normally a story like this would have me a-jitter with excitement. But for some reason, it fails to enthuse me.

So what’s up? Scientists have created (by means of an ingenious combination of intelligent design and natural selection) RNA molecules that can replicate. Except, well, personally I think “replicate” is rather a strong term. They copy themselves by assembling two smaller strings of RNA, rather than directly from nuclear acids (PZ Myers explains the process here). To me that doesn’t seem like that big a leap forward in the RNA World research. It’s one step in a long chain that might end up with something of supreme awesomeness - but we’re not there yet.

Cool stuff, but nothing I’d get overly excited about. (Or maybe I’m just stressed about the paper due on wednesday and having to turn my apartment upside down in anticipation of the new bed. Hard to tell with these things.)

evolution, rna