Religion as byproduct of useful cognitive processes

This is an excellent talk by Andy Thomson on the biological and psychological origins of religion.

It’s also precisely my position on the matter. There are many people who argue that religion provides a direct evolutionary advantage — I find them unconvincing. Thomson is explaining how religion’s origin is indirect, as a byproduct of properties of the brain that we find useful in modeling our world and social interactions…and religion is a parasite that hijacks these traits to promote a caricature of these properties.

(via Richard Dawkins)

I am Pro-Test

There was a rally in LA for a group in favor of animal experimentation, Pro-Test, which also had a counter-rally by animal rights groups. You can guess which side I’m on in this debate: blocking experimentation on animals would kill biological research dead. The tactics of the anti-vivisectionists are also reprehensible and deserving of condemnation.

The Pro-Test group, an offshoot of an Oxford, England-based group founded in 2006, was organized by J. David Jentsch, a UCLA neuroscientist who was the target of a recent attack by anonymous animal-rights activists.  In the attack, Jentsch’s car was set on fire while it was parked in front of his Westside home.  (The FBI recently announced that a reward for information leading to the arrest and conviction of those responsible has been increased to $75,000.)  Jentsch, who researches schizophrenia and drug addiction, conducts tests on monkeys.  While he acknowledges that some monkeys are killed as part of his research, he maintains that they do not suffer.  Jentsch was expected to speak at today’s rally.

Most importantly, we’re biologists. We’re in this business because we have a passion for the organisms we study, not because we’re some kind of sick sadists. We’re also currently swaddled up to our ears in regulations and monitors to prevent abuses of the animals in our care.

Unfortunately, the article discussing this rally has associated with it a poll. This makes me rather cranky—it’s a serious issue worth discussing, so please, don’t slap a stupid internet poll on it. It just means that advocacy groups will push at the numbers as if they mean something. So, please, go forth and destroy this pointless metric:

Can medical research on animals be conducted humanely?

Yes — and I support it if the animals are treated well 27% (1872 votes)

No — it’s inhumane by definition and I don’t support it 73% (5049 votes)

Not sure <1% (4 votes)

Puijila darwini

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

It’s yet another transitional fossil, everyone! Oooh and aaah over it, and laugh when the creationists scramble to pave it over with excuses.

What we have is a 23 million year old mammal from the Canadian arctic that would have looked rather like a seal in life…with a prominent exception. No flippers, instead having very large feet that were probably webbed. This is a walking seal.

i-2e998e366fcd8b430268a2fed96002fb-pujila.jpeg
(Click for larger image)

a, Palatal view of skull; b, lateral view of skull and mandible, left side; c, occlusal view of left mandible. Stippling represents matrix, hatching represents broken bone surface. The images are of three-dimensional scans. The brain case was scanned using computed tomography, whereas all other elements were surface scanned.

What it tells us is that marine pinnipeds almost certainly had an origin in the arctic, derived from terrestrial and semi-aquatic forms — these were more otter-like animals.

You’ll want to learn more about this beautiful creature. There is a website all about Puijila (in English, French, and Inuktitut) where you can find all kinds of images…and you can also find out how to pronounce “Puijila, something we’re all going to have to practice. Who knew paleontology was going to lead us all into learning a few words of Inuktitut?


Rybczynski N, Dawson MR, Tedford RH (2009) A semi-aquatic Arctic mammalian carnivore from the
Miocene epoch and origin of Pinnipedia. Nature 458:1021-1024.

Theoretical ecology of vampires

For some reason, I find this hilarious — it’s an exercise in applying the mathematics of population ecology to the dynamics of human-vampire interactions. It’s the real deal, the actual kinds of math used by those wacky evolution and ecology nerds, all built around some estimates of the rates of vampire siring measured against the rates that Buffy-style vampire slayers take them out. Here’s the kind of thing you’ll see in the document:

i-40ab1ceba09a7ced56a36f54f4e7dc5a-vampire_calc.jpeg

I like it. In case you’re wondering, Buffy’s Sunnyvale reaches a stable equilibrium with a population of about 36,000 humans and 18 vampires.

(Hmm. I posted this in the “Life Science” channel of scienceblogs. Maybe I need to lobby for an “Undead” channel now.)

Battle of the Biology Bands — no one leaves alive!

Perhaps you remember the PCR song from Bio-Rad…or perhaps you tried hard to purge that from your memory. Then Eppendorf upped the ante with a pipettor love song. Now Greg Laden finds another pop tribute to PCR from Bio-Rad. The genre? Disco. By all that’s good and rational, not disco.

Two can fight this war against good taste. How about a big hair rock ballad to a tissue culture cell monitoring system?

That one needs an encore.

Little known fact: most molecular biologists dress exactly like that in the lab.

Article up in the Guardian

My first column is up on the Guardian web site: it’s a brief introduction to asymmetries in snails, an abbreviated version of the post that I fleshed out with a little more detail.

I have to complain a little, though: the title says the observation of shared molecules between molluscs and humans “proves” we’re related. I really don’t like the use of the word “proof”, because it doesn’t — it is compatible with the hypothesis, or it supports the idea, but biologists don’t dabble in proofs.

There’s also an error on my part: I somehow transposed the stomach and liver. I know where these organs are, seriously — I teach part of an A&P course — so I blame my too-fast typing. Now no one is ever going to let me take a scalpel to their abdomen, ever.

Basics: Imprinting

I’ve been busy — I’m teaching genetics this term, and usually the first two thirds of the course is trivial to prepare for — we’re covering Mendelian genetics, and the early stuff is material the students have seen before and are at least generally familiar with the concepts, and all I have to do is cover them a little deeper and with a stronger quantitative component. That’s relatively easy.

The last part of the course, though, is where we start moving into uncharted waters for them, and every year I have to rethink how I’m going to cover the non-Mendelian concepts, and sometimes my ideas work well, and sometimes they don’t. If I teach it for another 20 years, I’ll eventually reach the point where every lecture has been honed into a comprehensible ideal. At least that’s my dream.

Anyway, one of the subjects we’re covering in the next lecture or two is imprinting, and I know from past experience that this can cause mental meltdowns in my students. This makes no sense if you’re used to thinking in Punnett squares! So I’ve been reworking this little corner of the class, and as long as I’m putting together a ground-up tutorial on the subject, I thought I might as well put it on the web. So here you are, a basic introduction to imprinting.

[Read more…]

Snails have nodal!

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

My first column in the Guardian science blog will be coming out soon, and it’s about a recent discovery that I found very exciting…but that some people may find strange and uninteresting. It’s all about the identification of nodal in snails.

i-9814996ee90947e59439af12f03a03db-nodal_guts.jpg

Why should we care? Well, nodal is a rather important — it’s a gene involved in the specification of left/right asymmetry in us chordates. You’re internally asymmetric in some important ways, with, for instance, a heart that is larger on the left than on the right. This is essential for robust physiological function — you’d be dead if you were internally symmetrical. It’s also consistent, with a few rare exceptions, that everyone has a stronger left ventricle than right. The way this is set up is by the activation of the cell signaling gene nodal on one side, the left. Nodal then activates other genes (like Pitx2) farther downstream, that leads to a bias in how development proceeds on the left vs. the right.

In us mammals, the way this asymmetry in gene expression seems to hinge on the way cilia rotate to set up a net leftward flow of extraembryonic fluids. This flow activates sensors on the left rather than the right, that upregulate nodal expression. So nodal is central to differential gene expression on left vs. right sides.

i-21bda85fe662c24fe34efc609dcbf4ac-nodal_cilia.jpg

What about snails? Snails are cool because their asymmetries are just hanging out there visibly, easy to see without taking a scalpel to their torsos (there are also internal asymmetries that we’d need to do a dissection to see, but the external markers are easier). The assymetries also appear very early in the embryo, in a process called spiral cleavage, and in the adult, they are obvious in the handedness of shell coiling. We can see shells with either a left-handed or right-handed spiral.

i-d03d89cba8e1ae44e04152b3d93bf105-nodal_spiral.jpeg
(Click for larger image)

Chirality in snails. a, Species with different chirality: sinistral
Busycon pulleyi (left) and dextral Fusinus salisbury (right). b, Sinistral (left)
and dextral (right) shells of Amphidromus perversus, a species with chiral
dimorphism. c, Early cleavage in dextral and sinistral species (based on ref.
27). In sinistral species, the third cleavage is in a counterclockwise direction,
but is clockwise in dextral species. In the next divisions the four quadrants
(A, B, C and D) are oriented as indicated. Cells coloured in yellow have an
endodermal fate and those in red have an endomesodermal fate in P. vulgata
(dextral)15 and B. glabrata (sinistral)28. L and R indicate left and right sides,
respectively. d, B. glabrata possesses a sinistral shell and sinistral cleavage
and internal organ organization. e, L. gigantea displays a dextral cleavage
pattern and internal organ organization, and a relatively flat shell
characteristic of limpets. Scale bars: a, 2.0 cm; b, 1.0 cm; d, 0.5 cm; e, 1.0 cm.

Until now, the only organisms thought to use nodal in setting up left/right asymmetries were us deuterostomes — chordates and echinoderms. In the other big (all right, bigger) branch of the animals, the protostomes, nodal seemed to be lacking. Little jellies, the cnidaria, didn’t have it, and one could argue that with radial symmetry it isn’t useful. The ecdysozoans, animals like insects and crustaceans and nematodes, which do show asymmetries, don’t use nodal for that function. This suggests that maybe nodal was a deuterostome innovation, something that was not used in setting up left and right in the last common ancestor of us animals.

That’s why this is interesting news. If a major protostome group, the lophotrochozoa (which includes the snails) use nodal to set up left and right, that implies that the ecdysozoans are the odd group — they secondarily lost nodal function. That would suggest then that our last common ancestor, a distant pre-Cambrian worm, used this molecule in the same way.

Look in the very early mollusc embryo, and there’s nodal (in red, below) switched on in one or a few cells on one side of the embryo, the right. It’s asymmetrical gene expression!

i-6daa81c2edebfc143fde371c4849c1cf-nodal_early_exp.jpeg
(Click for larger image)

Early expression of nodal and Pitx in snails. a, 32-cell stage L.
gigantea
expressing nodal in a single cell. b, Group of cells expressing Pitx in
L. gigantea. c, Onset of nodal expression in B. glabrata. d, A group of cells
expressing Pitx in B. glabrata. e, 32-cell L. gigantea expressing nodal (red) in
a single cell (2c) and brachyury (black) in two cells (3D and 3c).
f-h, brachyury (black) is expressed in a symmetrical manner in progeny of 3c
and 3d blastomeres (blue triangles in g), thus marking the bilateral axis, and
nodal (red) is expressed on the right side of L. gigantea in the progeny of 2c
and 1c blastomeres, as seen from the lateral (f) and posterior (g, h) views of
the same embryo. i, A group of cells expressing nodal (red) in the C quadrant
and Pitx (black) in the D quadrant of the 120-cell-stage embryo of L.
gigantea
. j, nodal (red) and Pitx (black) expression in adjacent areas of the
right lateral ectoderm in L. gigantea. L and R indicate the left and right sides
of the embryo, respectively. The black triangle in b and i, the green, yellow
and pink arrows in f and i, and the black and pink arrows in f and h point to
the equivalent cells. Scale bars: 50µm.

Seeing it expressed is tantalizing, but the next question is whether it actually does anything in these embryos. The test is to interfere with the nodal-Pitx2 pathway and see if the asymmetry goes away…and it does, in a dramatic way. There is a chemical inhibitor called SB-431542 that disrupts this pathway, and exposing embryos to it does interesting things to the formation of the shell. In the photos below, the animal on the left is a control, and what you’re seeing is a coiled shell (opening to the right). The other two views are of an animal treated with SB-431542…and look! Its shell doesn’t have either a left- or right-handed twist, and instead extends as a straight tube.

i-055b648d0eaf32f767e5cc31f9f9a19b-nodal_shell.jpeg
(Click for larger image)

Wild-type coiled and drug-treated non-coiled shells of B.
glabrata
.
Control animals
(e) display the normal sinistral shell morphology. Drug-treated animals
(f, g, exposed to SB-431542 from the 2-cell stage onwards) have straight
shells. f and g show an
individual, ethanol-fixed, and shown from the side (f) and slightly rotated
(g).

What this all means is that we’ve got a slightly better picture of what genes were present in the ancestral bilaterian animal. It probably had both nodal and Pitx2, and used them to build up handedness specializations. Grande and Patel spell this out:

Although Pitx orthologues have also been identified in non-deuterostomes such as Drosophila melanogaster and
Caenorhabditis elegans, in these species Pitx has not been reported in
asymmetrical expression patterns. Our results suggest that asymmetrical expression of Pitx might be an ancestral feature of the bilaterians.
Furthermore, our data suggest that nodal was present in the common
ancestor of all bilaterians and that it too may have been expressed
asymmetrically. Various lines of evidence indicate that the last common ancestor of all snails had a dextral body. If this is true, then our
data would suggest that this animal expressed both nodal and Pitx on
the right side. Combined with the fact that nodal and Pitx are also
expressed on the right side in sea urchins, this raises the possibility
that the bilaterian ancestor had left-right asymmetry controlled by
nodal and Pitx expressed on the right side of the body. Although
independent co-option is always a possibility, the hypotheses we present can be tested by examining nodal and Pitx expression and function in a variety of additional invertebrates.

It’s also, of course, more evidence for the unity of life. We are related to molluscs, and share key genes between us.


Grande C, Patel NH (2009) Nodal signalling is involved in left-right asymmetry in snails. Nature 457(7232):1007-11.

Cephalopod venoms

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

The history of venoms is a wonderful example of an evolutionary process. We’re all familiar with the idea of venomous snakes, but the cool thing is that when we examine exactly what it is they’re injecting into their prey, it’s a collection of proteins that show a nested hierarchy of descent. Ancient reptiles had a small and nasty set of poisons they would use, and to improve their efficacy, more and more have been added to the cocktail; so some lizards produce venomous proteins, while the really dangerous members of the Serpentes produce those same proteins, plus a large array of others.

i-6cf230da0ba5a3497fce1fd797019ad6-lizard_venoms.jpg

So something like CRISP (Cystein RIch Secretory Protein) is common to all, but only the most refined predators add PLA2 (Phosopholipase A2) to the mix.

Now lethally poisonous snakes are nice and cute and all, but we all know where the interesting action really is: cephalopods. Let’s leave the vertebrates altogether and look at a venomous protostome clade to see what they do.

i-ff97caf7d7970f57aa4b6dc82eace617-ceph_venom_glands.gif
Relative glandular arrangements of a cuttlefish and b octopus. Posterior gland is shown in green; anterior, in blue. Orange structure is the beak.

Brian Fry, who did all that excellent work characterizing and cataloging the
pharmacy of venoms secreted by poisonous snakes, has also turned his hand to the cephalopods. He examined the products of the venom glands of octopus, squid, and cuttlefish, and found a range of proteins, some unique, and others familiar: CAP (a CRISP protein), chitinase, peptidase S1, PLA2 and others. There are a couple of interesting lessons in that list.

First, evolution doesn’t just invent something brand new on the spot to fill a function — what we find instead is that existing proteins are repurposed to do a job. This is how evolution generally operates, taking what already exists and tinkering and reshaping it to better fulfill a useful function. Phospholipase A2, for instance, is a perfectly harmless and extremely useful non-venomous protein in many organisms — we non-toxic humans also make it. We use it as a regulatory signal to control the inflammation response to infection and injury — in moderation, it’s a good thing. What venomous animals can do, though, is inject us with an overdose of this regulator to send our local repair and recovery systems berserk, producing swelling that can incapacitate a tissue. Similarly, a peptidase is a useful enzyme for breaking down proteins in the digestive system…but a poisonous snake or cephalopod biting your hand can squirt it into the tissues, and now it’s being used to digest your muscles and connective tissue. Some effective venoms are simply common proteins used inappropriately (from the perspective of the target).

Another interesting observation is that cephalopods and vertebrates have independently converged in using some of the same venoms. In part, this is a consequence of historical availability — all animals have phospholipases,, since they are important general signalling molecules, so it’s part of the collection of widgets in the metazoan toolbox from which evolution can draw. It’s also part of an inflammation pathway that can be exploited by predators, in the same way that we have shared proteins used in the operation of the nervous system that can be targeted by neurotoxins. So there is independent convergence on a specific use of these proteins as toxins, but one of the things that facilitates the convergence is a shared ancestry.

In fact, some very diverse groups seem to consistently settle on the same likely suspects in their venoms.

i-427acefb14a1c22ea42a523485acea91-venom_table.gif

But finally, there must also be physical and chemical proteins of these particular proteins that must also predispose them to use as toxins. After all, animals aren’t coopting just any protein for venoms — they aren’t injecting large quantities of tubulin or heat shock proteins into their prey. There must be something about each of the standard suspects in venoms that make them particularly dangerous. What the comparative evolutionary approach allows us to do is identify the common molecular properties that make for a good venom. As Fry explains it,

Typically the proteins chosen are from
widely dispersed multigene secretory protein families with
extensive cysteine cross-linking. These proteins are collectively much more numerous than globular enzymes,
transmembrane proteins, or intracellular protein. Although
the relative abundance of these protein types in animal
venoms may reflect stochastic recruitment processes, there
has not been a single reported case of a signal peptide
added onto a transmembrane or intracellular protein or a
hybrid protein expressed in a venom gland. A strong bias is
also evident for all of the protein-scaffold types, whether
from peptides or enzymes. Although the protein scaffolds
present in venoms represent functionally and structurally
versatile kinds, they share an underlying biochemistry that
would produce toxic effects when delivered as an “overdose”. Toxic effects include taking
advantage of a universally present substrate to cause
physical damage or causing changes in physiological
chemistry though agonistic or antagonistic targeting. This allows the new venom gland protein to have an
immediate effect based on overexpression of the original
bioactivity. Furthermore, the features of widely dispersed
body proteins, particularly the presence of a molecular
scaffold amenable to functional diversification, are features
that make a protein suitable for accelerated gene duplication and diversification in the venom gland.

To simplify, killing something with a secreted poison typically involves reusing an extant protein, but not just any protein — only a subset of the proteins in an animal’s proteome has just the right properties to make for a good venom. Therefore, we see the same small set of proteins get independently coopted into the venom glands of various creatures.


Fry BG, Roelants K, Norman JA (2009) Tentacles of venom: toxic protein convergence in the Kingdom Animalia. J Mol Evol Mar 18. [Epub ahead of print].