Cats, candy, and evolution

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Here’s a small taste of Roald Dahl’s Charlie and the Chocolate Factory, a sweet story about a poor boy and his visit to an amazing candy factory…you’ve probably heard of it, since the new movie is getting a lot of press.

Only once a year, on his birthday, did Charlie Bucket ever get to taste a bit of chocolate. The whole family saved up their money for that special occasion, and when the great day arrived, Charlie was always presented with one small chocolate bar to eat all by himself. And each time he received it, on those marvelous birthday mornings, he would place it carefully in a small wooden box that he owned, and treasure it as though it were a bar of solid gold; and for the next few days, he would allow himself only to look at it, but never to touch it. Then at last, when he could stand it no longer, he would peel back a tiny bit of the paper wrapping at one corner to expose a tiny bit of chocolate, and then he would take a tiny nibble—just enough to allow the lovely sweet taste to spread out slowly over his tongue. The next day, he would take another tiny nibble, and so on, and so on. And in this way, Charlie would make his ten-cent bar of birthday chocolate last him for more than a month.i-a420ae8c62e074dde7e2fce0652d306e-tinystop.gif

That’s how it is published, at any rate. What if it read something like this?

Only once a year, on his birthday, did Charlie Bucket ever get to taste a bit of chocolate. The whole family saved up their money for that special occasion, and when the great day arrived, Charlie was always presented with one small chocolate bar to eat all by himself. And each time he received it, on those marvelg ynfg, jura ur pbhyq fgnaq vg ab ybatri-a420ae8c62e074dde7e2fce0652d306e-tinystop.gif, ur jbhyq i-a420ae8c62e074dde7e2fce0652d306e-tinystop.gifrry onpx n gval ovg bs gur cncre jenccvat ng bar pbeare gb rkcbfr n gval ovg bs pubpbyngr, naq gura ur jbhyq gnxr n gval avooyr-whfg rabhtu gb nyybj gur ybiryl fjrrg gnfgr gb fcernq bhg fybjyl bire uvf gbathr. Gi-a420ae8c62e074dde7e2fce0652d306e-tinystop.gifr arkg qnl, ur i-a420ae8c62e074dde7e2fce0652d306e-tinystop.gifbhyq gnxr nabgure gval avooyr, naq fb ba, naq fb ba. Naq va guvf jnl, Puneyvr ji-a420ae8c62e074dde7e2fce0652d306e-tinystop.gifhyq znxr uvf gra-prag one bs oveguqnl pubpbyngr ynfg uvz sbe zber guna n zbagu.

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Hox cluster disintegration

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Hox genes are metazoan pattern forming genes—genes that are universally associated with defining the identities of regions of the body. There are multiple Hox genes present, and one of their unusual properties is that they are clustered and expressed colinearly. That is, they are found in ordered groups on the chromosome, and that the gene on one end is typically turned on first and expressed at the head end of the embryo, the next gene in order is turned on slightly later and expressed further back, and so on in sequence. That the tidy sequential order on the chromosome is associated with an equally tidy spatial and temporal pattern of expression in the body has always been one of the more fascinating aspects of these genes, and they are one of the few cases where we see an echo of phenotypic form comprehensibly laid out in the DNA.

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Palaeos reborn!

First I reported that Palaeos was lost, and then that it might be found, but now it looks like we can safely say it is being reborn. The old version of Palaeos has been at least partially restored, but the really important news is that a Palaeos wiki has been set up and people are working on reassembling old content and creating new information in a much more flexible format. If you’ve got some phylogenetic or palaeontological expertise, you might want to consider joining the Palaeos team and helping out with this big project.

3.3 million years old, 3 years old

Say hello to Selam, or DIK-1-1, a new and very well preserved member of the family discovered in Dikika, Ethiopia. She belongs to the species Australopithicus afarensis and is being called Lucy’s little sister.

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She was only a toddler when she died about 3.3 million years ago, and from the teeth the authors estimate that she was about 3 years old. Most of the skeleton is intact, but doesn’t seem to have yet been fully extracted from the matrix.

Some of the surprises: the hyoid bone is chimpanzee-like, and implies chimp-like vocalization abilities. She had a long way to go before she could have a conversation. The fingers are long and curved, and the scapula is more gorilla-like than ours; there is a suggestion of better arboreal ability than we have.


Alemseged Z, Spoor F, Kimbel WH, Bobe R, Geraads D, Reed D, Wynn JG (2006) A juvenile early hominin skeleton from Dikika, Ethiopia. Nature 443:296-301.

Rhabdomeric and ciliary eyes

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We are all familiar with the idea that there are strikingly different kinds of eyes in animals: insects have compound eyes with multiple facets, while we vertebrates have simple lens eyes. It seems like a simple evolutionary distinction, with arthropods exhibiting one pattern and vertebrates another, but the story isn’t as clean and simple as all that. Protostomes exhibit a variety of different kinds of eyes, leading to the suggestion that eyes have evolved independently many times; in addition, eyes differ in more than just their apparent organization, and there are some significant differences at the molecular level between our photoreceptors and arthropod photoreceptors. It’s all very confusing.

There has been some recent press (see also this press release from the EMBL) about research on a particular animal model, the polychaete marine worm, Platynereis dumerilii, that is resolving the confusion. The short answer is that there are fundamentally two different kinds of eyes based on the biology of the cell types, and our common bilaterian ancestor had both—and the diversity arose in elaborations on those two types.

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Patterning the nervous system with Bmp

I’m a little surprised at the convergence of interest in this news report of a conserved mechanism of organizing the nervous system—I’ve gotten a half-dozen requests to explain what it all means. Is there a rising consciousness about evo-devo issues? What’s caused the sudden focus on this one paper?

It doesn’t really matter, I suppose. It’s an interesting observation about how both arthropods and vertebrates seem to partition regions along the dorso-ventral axis of the nervous system using exactly the same set of molecules, a remarkable degree of similarity that supports the idea of a common origin. Gradients of a molecule called Bmp may be the primitive mechanism for establishing dorso-ventral polarity in animals.

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Palaeos found?

I got this email from Alan Kazlev, one of the main fellows working on the Palaeos website (a very useful paleontological resource), which I had previously reported as going offline. Plans are afoot to bring it back, and the answer seems to be to wikify it and build it anew, with a more distributed set of contributors. How Web 2.0! I’ve included the full email below the fold if you’d like more details.

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What? No cephalopod genome project?

I was reading a review paper that was frustrating because I wanted to know more—it’s on the evolution of complex brains, and briefly summarizes some of the current confusion about what, exactly, is involved in building a brain with complex problem solving ability. It’s not as simple as “size matters”—we have to jigger the formulae a fair bit to take into account brain:body size ratios, for instance, to get humans to come out on top, and maybe bulk is an inaccurate proxy for more significant matters, such as the number of synapses and nerve conduction velocities.

There’s also a growing amount of literature that takes genomic approaches, searching for sequences that show the signatures of selection, and plucking those out for analysis. There have been some provocative results from that kind of work, finding some candidate genes like ASPM, but another of the lessons of that kind of work seems to be that evolution has been working harder on our testis-specific genes than on our brains.

The encouraging part of the paper is that the authors advocate expanding our search for the correlates of intelligence with another group of organisms with a reputation for big brains, but brains that have evolved independently of vertebrates’. You know what I’m talking about: cephalopods!

The Cephalopoda are an ancient group of mollusks originating in the late Cambrian. Ancestors of modern coleoid cephalopods (octopus and squid) diverged from the externally-shelled nautiloids in the Ordovician, with approximately 600 million years of separate evolution between the cephalopod and the vertebrate lineages. The evolution of modern coleoids has been strongly influenced by competition and predatory pressures from fish, to a degree that the behavior of squid and octopus are more akin to that of fast-moving aquatic vertebrates than to other mollusks. Squid and octopuses are agile and active animals with sophisticated sensory and motor capabilities. Their central nervous systems are much larger than those of other mollusks, with the main ganglia fused into a brain that surrounds the esophagus with additional lateral optic lobes. The number of neurons in an adult cephalopod brain can reach 200 million, approximately four orders of magnitude higher than the 20-30,000 neurons found in model mollusks such as Aplysia or Lymnaea. Cephalopods exhibit sophisticated behaviors a number of studies have presented evidence for diverse modes of learning and memory in Octopus and cuttlefish models. This learning capacity is reflected in a sophisticated circuitry of neural networks in the cephalopod nervous system. Moreover, electrophysiological studies have revealed vertebrate-like properties in the cephalopod brain, such as compound field potentials and long-term potentiation. Thus cephalopods exhibit all the attributes of complex nervous systems on the anatomical, cellular, functional and behavioral levels.

Unfortunately, the purpose of the paper is to highlight an unfortunate deficiency in our modern research program: there is no cephalopod genome project. The closest thing to it is an effort to sequence the genome of another mollusc, Aplysia, which is a very good thing—Aplysia is a famous and indispensable subject of much research in learning and memory—but it’s no squid. The authors are advocating additional work on another animal, one with a more elaborate brain.

A parallel effort on a well-studied octopus or squid should provide insights on the evolutionary processes that allowed development of the sophisticated cephalopod nervous system. For example, have cephalopods undergone accelerated evolution in specific nervous system genes, as has been suggested for primates? Have specific gene families undergone expansion in the cephalopod lineage and are these expressed in the nervous system? Are there clear parallels in accelerated evolution, gene family expansion, and other evolutionary processes between cephalopods and vertebrates? Answers to these and related questions will provide useful perspectives for evaluation of the processes thought to be involved in the evolution of the vertebrate brain.

I’m all for it—let’s see a Euprymna genome project!

Jaaro H, Fainzilber M (2006) Building complex brains—missing pieces in an evolutionary puzzle. Brain Behav Evol 68(3):191-195.

MnCSE!

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Good news for Minnesota! Minnesota Citizens for Science Education has been officially launched. This is a new advocacy group with the goal of promoting good science education in our state. Specifically—

A scientifically literate population is essential to Minnesota’s future. To that end, Minnesota Citizens for Science Education (MnCSE) will bring together the combined resources of teachers, scientists, and citizens to assure, defend, and promote the teaching and learning of evolutionary biology and other sciences in K-12 public school science classrooms, consistent with current scientific knowledge, theories, and practice.

If you’d like to be more involved, join the group. Browse the personal statements of the science advisors. Come on down to Science Education Saturday at the Bell Museum, on 11 November.

Oh, and if you like the logo, buy it on a t-shirt or coffee mug.