The carpenter and the pyromaniac

A very familiar story: a creationist is told that her views are unsupported by any legitimate science, and in reply she rattles off a list of creationist “scientists”.

Here we are told by a creationist housewife — as she describes herself — defending her belief that the Giant’s Causeway is only as old as the Bible says it is, a claim which assumes, of course, that there is a definite chronology in the Bible which can be used to date the age of the earth, and that this chronology, such as it is, supersedes all other forms of chronology, because the Bible is, after all, the inerrant word of God. In response to Richard Dawkins claim that reputable scientists all agree that the earth is billions of years old, our doughty housewife responds with: “That’s a blatant lie,” And then she lists four “scientists” who accept the creationist dating of the age of the earth (and she might well have named more, because, if you google these names, you end up on sites with many more).

The word “scientist” is simply a label, and if you ignore its meaning, you can stick it on anything. I’ve always considered a scientist as someone who follows a rational program of investigation of the real world, and that the word describes someone carrying out a particular and critical process of examination. But apparently, to people with no well-informed knowledge of its meaning, “science” and “scientist” are just tags you stick on really smart people who reach a conclusion you like, or who have done the academic dance to get a Ph.D. as a trophy to stick on the end of your name.

That’s a shame.

Let me explain the difference with an analogy.

A carpenter is a person who practices a highly skilled trade, carpentry, to create new and useful and lovely things out of wood. It is a non-trivial occupation, there’s both art and technology involved, and it’s a productive talent that contributes to people’s well-being. It makes the world a better place. And it involves wood.

A pyromaniac is a person with a destructive mental illness, in which they obsess over setting things on fire. Most pyromaniacs have no skill with carpentry, but some do; many of them have their own sets of skills outside of the focus of their illness. Pyromania is destructive and dangerous, contributes nothing to people’s well-being, and makes the world a worse place. And yes, it involves wood, which is a wonderful substance for burning.

Calling a creationist a scientist is as offensive as praising a pyromaniac for their skill at carpentry, when all they’ve shown is a talent for destroying things, and typically have a complete absence of any knowledge of wood-working. Producing charcoal and ash is not comparable to building a house or crafting furniture or, for that matter, creating anything.

You can’t call any creationist a scientist, because what they’re actively promoting is a destructive act of tearing down every beautiful scrap of knowledge the real scientists have acquired.

Brains and beaks

I’m always telling people you need to understand development to understand the evolution of form, because development is what evolution modifies to create change. For example, there are two processes most people have heard of. One is paedomorphosis, the retention of juvenile traits into adulthood — a small face and large cranium are features of young apes, for instance, and the adult human skull can be seen as a child-like feature. A complementary process is peramorphosis, where adult characters appear earlier in development, and then development continues along the morphogenetic trajectory further than normal, producing novel attributes. You may have encountered examples of this in fiction: the best known are the Pak Protectors in Niven’s science-fiction stories, which are the result of longer-lived humans continuing the processes of aging to reach a novel form. There’s also the story of After Many a Summer Dies the Swan, a novel by Aldous Huxley, in which a paedomorphic species (a human) lives for a very long time and develops to reach the ancestral state — a more primitive apelike form.

Just to make it more complicated, though, this isn’t to say that evolution proceeds by arresting the whole of development, turning the adult into an overgrown baby. What’s going on here is that genes that control the rate of development are being tweaked by genetic change, and there are many of those genes. There can be all sorts of mixing and matching — one organ or feature can undergo paedomorphosis in a species at the same time that another is undergoing peramorphosis.

A beautiful example has recently been published in Nature: the evolution of the avian skull. The postcranial bird skeleton can’t be neatly categorized as changes in rate: wings, the correlated changes in the pelvis and thorax, all that is a messy collection of novelties. The skull, though, can at least be broken down into a couple of key avian adaptions: brains and beaks. The cranium has gone through a set of changes with all the behavioral and sensory changes (big eyes, motor aspects of flight, navigation), while the beak has obviously diversified for different feeding strategies. The beak has changed to take over the manipulatory role lost as forelimbs became wings.

Here’s how the role of heterochrony (changes in rate of development) of different species was determined. The authors collected quantitative morphological data on a set of fossil dinosaurs and birds and extant birds for which there were both embryological and adult data. There are some straightforward observations that just leap out at you. For instance, embryonic alligator skulls have the same proportions as the skull of adult Confuciusornis, a crow-sized bird from the Cretaceous.


Similarity of embryonic Alligator and adult Confuciusornis skulls. Superimposition of Alligator embryo skull (green) onto Alligator adult skull (red, left) and onto Confuciusornis adult skull (red, right), showing the nearly identical skull configuration of the latter two and indicating paedomorphic cranial morphology in Confuciusornis.

Another common and long-hallowed technique in developmental biology is to trace a standard skull onto a 2-D grid and then determine what distortions of the grid are necessary to reshape the skull into a specific form. This method makes the stretching and skewing and compression that had to have occurred over time to sculpt these skulls from an ancestor. Here are the ontogenetic changes for different species, illustrating how they changed shape as they grew up.


Summary of ontogenetic changes in archosaur skulls; outlines on deformation grids from average. a, Alligator. b, Compsognathidae. c, Therizinosauridae. d, Archaeopteryx. e, Enantiornithes. f, Confuciusornis. g, Ostriches (Struthio).

If you can do this kind of assessment of transformations over development, you can also do it over phylogeny. Below are shown the trends observed in dinosaur and avian evolution.


Summary of heterochrony and phylogeny in bird skull evolution. emu Dromaius. Heterochronic transformations referred to in the text are A phylogenetic sequence with skull outlines set on deformation grids is enumerated with Roman numerals. Major anatomical regions involved in depicted from the primitive stem-group archosaur Euparkeria to the modern heterochronic transformations are labelled.

The coordinate system on which those skulls are mapped is a little tricky to explain. With all the numerical data available from their skull measurements, the authors did a principal component analysis, determining metrics that accounted for most of the variability between skulls. What they found were two axes of change: one is in the shape of the cranium, which exhibited paedomorphic patterns of change (although the contents of that cranium, the brain, is known to have undergone more complex heterometric change); the second was in the beak, which shows a pattern of peramorphic change.

But that’s the cool thing about this! We can quantitatively describe the plastic changes in the shape of the skull over evolutionary history as largely the product of two trends: a retention of the bulbous embryonic shape of the skull, and increased extension of the facial bones to form a beak. It’s not magic, it’s the expected incremental shifts in shape over long periods of time, in which we can actually visualize the pattern of transformation.

Now we just need to work out the genes behind these morphological changes, and their mode of action. That’s all. Hey, I think the developmental biologists have at least a century of gainful employment ahead of them…

Bhullar BA, Marugán-Lobón J, Racimo F, Bever GS, Rowe TB, Norell MA, Abzhanov A (2012) Birds have paedomorphic dinosaur skulls. Nature doi: 10.1038/nature11146. [Epub ahead of print]

Hello, Washington DC and CFI!

I’m going to be doing a bit of traveling again starting in August. I’ll be in Washington DC on the 18th, to do a fundraiser lunch for CFI-DC, and I’ll also be doing a talk later that afternoon. The talk title is “Life is Chemistry“, and I’ll be explaining why material causes are sufficient to explain this phenomenon we call life — no ghosts, spirits, souls, or magic Frankensteins in the sky to make it all happen.

Sign up for tickets now! Last time I was there they sold out.

Swimming in the Cambrian

If you ever get a chance, spend some time looking at fish muscles in a microscope. Larval zebrafish are perfect; they’re transparent and you can trace all the fibers, so you can see everything. The body musculature of fish is most elegantly organized into repeating blocks of muscle along the length of the animal, each segment having a chevron (“V”) or “W” shape. Here’s a pretty stained photo of a 30 hour old zebrafish to show what I mean; it’s a little weird because this one is from an animal with experimentally messed up gene expression, all that red and green stuff, but look at the lovely blue muscle fibers stretching across the length of each segment.


Lateral view of a 30 hour old zebrafish, embryonic myotome, displaying ectopic eng2a:eGFP (green) fibers in response to Smad7 (marked in red) expressing clones. Slow muscle fibers are marked by monoclonal antibody F59 (blue).

But wait—why the chevron shape? Also, the reason I told you to look in a microscope sometime is that a 2-D image can’t illustrate the lovely intricacy of the muscles; they don’t go straight across, but twist in a partial spiral in 3-dimensions. Trust me, it’s beautiful to see. And it’s also nearly universal in chordates — even Amphioxus has this arrangement. And there’s a good biomechanical reason for this arrangment.

[Read more…]

Have they got a Higgs boson?

Sean Carroll live-blogged a seminar discussing the latest results, which meant he wrote down a heck of a lot of cryptic jargon I couldn’t understand at all. But here’s the bottom line:

Personal editorializing by me: we’ve found the Higgs, or at least a Higgs. Still can’t be sure that it’s just the vanilla Standard Model Higgs. The discrepancies aren’t quite strong enough to be sure that they really represent beyond-Standard-Model physics… but it’s a strong possibility.

Cool. The broad strokes of the Standard Model look OK, but there might be enough unexpected variance that some new physics will emerge from it all. It sounds like the best of all possible results from a physicist’s point of view.

But really, the best part of the article was this: