I was sitting down this evening to write up this nifty new paper from the Carroll lab, when I noticed that Carl Zimmer beat me to it. Dang. There are all these other bloggers around here, and it’s hard to keep on top of all of them, all at once.
Go read it anyway. It’s good stuff, all about the importance of regulatory changes in evolution.
Early Cambrian shrimp! I just had to share this pretty little fellow, a newly described eucrustacean from the lower Cambrian, about 525 million years ago. It’s small — the larva here is about 1.8mm long, and the adults are thought to have been 3mm long — but it was probably numerous, and I like to imagine clouds of these small arthropods swarming in ancient seas.
I’ve written a long introduction to the work I’m about to describe, but here’s the short summary: the parts of organisms are interlinked by what has historically been called laws of correlation, which are basically sets of rules that define the relationship between different characters. An individual attribute is not independent of all others: vary one feature, and as Darwin said, “other modifications, often of the most unexpected nature, will ensue”.
Now here’s a beautiful example: the regulation of the growth of mammalian molars. Teeth have long been a useful tool in systematics—especially in mammals, they are diverse, they have important functional roles, and they preserve well. They also show distinct morphological patterns, with incisors, canines, premolars, and molars arranged along the jaw, and species-specific variations within each of those tooth types. Here, for example, is the lower jaw of a fox. Look at the different kinds of teeth, and in particular, look at the differences within just the molars.
Note that in this animal, there are three molars (the usual number for most mammals, although there are exceptions), and that the frontmost molar, M1, is the largest, M2 is the second largest, and M3, the backmost molar, is the smallest. This won’t always be the case! Some mammals have a larger M3, and others may have three molars of roughly equal size. What rules regulate the relative size of the various molars, and are there any consistent rules that operate across different species?
To answer those questions, we need to look at how the molars develop, which is exactly what Kavanagh et al. have done.
John Dennehy’s citation classic this week is The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme, by Gould and Lewontin. It’s one of my favorite papers of all time — if you haven’t read it, you should do so now. It contains a set of ideas that are essential to understanding evo-devo.
Gould always struck me as a closet developmental biologist — he should have studied it more!
Cuvier, and his British counterpart, Richard Owen, had an argument against evolution that you don’t hear very often anymore. Cuvier called it the laws of correlation, and it was the idea that organisms were fixed and integrated wholes in which every character had a predetermined value set by all the other characters present.
In a word, the form of the tooth involves that of the condyle; that of the shoulder-blade; that of the claws: just as the equation of a curve involves all its properties. And just as by taking each property separately, and making it the base of a separate equation, we should obtain both the ordinary equation and all other properties whatsoever which it possesses; so, in the same way, the claw, the scapula, the condyle, the femur, and all the other bones taken separately, will give the tooth, or one another; and by commencing with any one, he who had a rational conception of the laws of the organic economy, could reconstruct the whole animal.
Cuvier famously (and incorrectly) argued that he could derive the whole of the form of an animal from a single part, and that this unity of form meant that species were necessarily fixed. An organism was like a complex, multi-part equation that used only a single variable: you plugged a parameter like ‘ocelot’ into the Great Formula, and all the parts and pieces emerged without fail; plug in a different parameter, say ‘elephant’, and all the attributes of an elephant would be expressed. By looking at one element, such as the foot, you could determine whether you were looking at an elephant or an ocelot, and thereby derive the rest of the animal.
Tristero makes a few points that are exactly what I’ve been trying to get across in my introductory biology class this week, where we’re covering Charles Darwin and the evidence for evolution. The first is that we do not rely on Darwin’s authority; there is no cult of personality, no reliance on the master’s word, no simple trust of anything or anyone. The other, though, is that Darwin is still a fascinating and important figure, and it’s not just that he was an old guy with a white beard who lectured the law.
Darwin’s not a stuff-shirted Nigel Bruce pip-pipping his way across the Empire. He is a young kid on a ship who once had the gall to grab a sailor’s dinner from his plate because he (the sailor) was about to eat a very rare ostrich Darwin had been searching for in vain for months. He’s a fellow who, when learning to use the bolas from Argentinian gauchos, managed to lasso his own horse, and he’s willing to write about it. Later, as he worked through his theory, which took him over 20 years to announce, he was tormented by the implications if it was misconstrued (as it was, right from the beginning). He developed a cautious style that is a model of arguing and inferring from the evidence. And, by all accounts, Darwin was a man devoted to his family and friends, deeply considerate and generous.
Yes, Darwin had his faults. But anyone with ten times his faults and one tenth of his talent would easily win a Nobel or Macarthur. That kids don’t have a chance to learn who this guy was – that’s a real crime.
One thing I tried to get across to my students was how much he was like them. He went off to Cambridge when he was about their age, and on graduation, a position they’ll all be in in a few years, had to wheedle his father into letting him go on this exotic sea voyage instead of settling down. Darwin really was a young fellow when he went off on the Beagle, in his early twenties.
Despite his charming youth, though, I still have to explain the list of things he got right and the list of things he got wrong. It’s the evidence and the ideas that matter, not the lovely personality behind them.
All of us mammals have pretty much the same set of genes, yet obviously there have to be some significant differences to differentiate a man from a mouse. What we currently think is a major source of morphological diversity is in the cis regulatory regions; that is, stretches of DNA outside the actual coding region of the gene that are responsible for switching the gene on and off. We might all have hair, but where we differ is when and where mice and men grow it on their bodies, and that is under the control of these regulatory elements.
A new paper by Fondon and Garner suggests that there is another source of variation between individuals: tandem repeats. Tandem repeats are short lengths of DNA that are repeated multiple times within a gene, anywhere from a handful of copies to more than a hundred. They are also called VNTRs, or variable number tandem repeats, because different individuals within a population may have different numbers of repeats. These VNTRs are relatively easy to detect with molecular tools, and we know that populations (humans included) may carry a large reservoir of different numbers of repeats, but what exactly the differences do has never been clear. One person might carry 3 tandem repeats in a particular gene, while her neighbor might bear 15, with no obvious differences between them that can be traced to that particular gene. So the question is what, if anything, does having a different number of tandem repeats do to an organism?
Here’s a website of mutating pictures, a collection of images made with a splatter of scattered triangles. Your job is to browse through them and score them for how much they resemble a face — which isn’t easy. If I stare at any random pile of symmetrical shadings, they all start to look like faces to me.
Anyway, pictures that get higher scores produce more progeny, with slight mutations, in the next round of picture generation. You can see where this is going…
One concept that is sometimes used in developmental biology is the idea of the “master control gene” or “master switch” — a single gene whose expression is both necessary and sufficient to trigger activation of many other genes in a coordinated fashion, leading to the development of a specific tissue or organ. It’s a handy concept on which to hang a discussion of transcription factors, but it may actually be of rather limited utility in the real world of molecular genetics: there don’t seem to be a lot of examples of master control genes out there! Pax-6 is the obvious one, a gene that initiates development of the eye, and other genes may be mentioned in certain stem cell pathways, but even in the eyes of vertebrates, for example, eye development is more complicated than a single switch, and similarly, many other developmental processes seem to use multiple or redundant regulatory controls — the cases where we have a single gene bottleneck are either rare or poorly represented in the literature.
They’re still at least pedagogically useful, though — it’s a simple case of imposition of a specific developmental pathway on a patch of tissue.
T. Ryan Gregory is turning into quite the coiner of useful terms. The latest: Dog’s Ass Plots. It refers specifically to charts that try to make a case for the evolution of complexity by selectively encoding their creator’s assumptions about the topic, and especially by oversimplifying the data in a way that skews their interpretation.
I suspect DAPs are a problem in other fields as well, though.
