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].

Nebraska faces limited choices

A retraction: I’ve talked with Lanny Boswell, and he is most definitely NOT a creationist. I’ve edited the post below.


Candidates are busy running for election to the Lincoln school board in Nebraska right now, and guess what’s been found? Creationists! Running for election! A newspaper story neatly summarizes the positions of many of the candidates, and here is a set you Nebraskans should not vote for.

  • Kevin Keller “wished creationism was taught in place of evolution, but should at least be taught alongside evolution”…although now that he has been exposed, he is frantically backtracking.

  • “Kirby Young, a candidate for the District 1 seat, and Andrew Ringsmuth, a candidate for the District 7 seat, said creationism should be taught as a theory alongside evolution.”

  • “Gregory Wiltshire, a candidate for the District 1 seat, said he doesn’t believe creationism should be taught in science classes, but schools should give students the chance to explore their interest in creationism.”

  • “Norman Dority, seeking the District 5 seat, said schools should present theories of creationism and evolution but should not dictate how they are taught.”

  • “Andrew Ringsmuth: candidate for District 7 seat: Ringsmuth said, at the high school level, evolution should be taught as a theory that many, but not all, scientists support. He said teachers should be allowed to give students a chance to explore creationism, intelligent design and evolution and decide for themselves which theory they support.”

Keller is a particularly interesting case: he was endorsed by the Lincoln Education Association’s PAC. They’re trying to rationalize it away now, but I think they should send a clearer message and remove their endorsement. I’m sorry, but people as ignorant as the ones listed above have no place in managing a school system.

All is not lost — there are a few candidates with sensible positions. These are the ones you should vote for, Nebraska.

  • “Kathy Danek: candidate for re-election to her District 1 seat: She doesn’t support incorporating creationism, which she considers a religious belief, in science curriculum. She said she could see creationism being used as a topic in a student debate class or activity.”

  • “Barb Baier: candidate for District 3 seat: Baier said creationism should not be taught in science classes. She said she considers it a philosophy, not a form of science, but could see it being taught in a philosophy or literature course.”

  • “Don Mayhew: candidate for re-election to his district 7 seat: Mayhew said neither creationism nor intelligent design is based on the scientific method and that he doesn’t support teaching either concept in science classes.”

  • “Lanny Boswell, a candidate for the District 5 seat, said creationism shouldn’t be taught in science classes, but those classes should teach students to be critical thinkers and consider divergent viewpoints.”

Three Four people gave good answers, and four seats are open. It sounds like at least one useless dingleberry is going to get a voice in Nebraska education.

Hey, in addition to voting for pro-science candidates, maybe a few more of you scientifically minded Nebraskans need to start running for these positions. The kooks always seem anxious to rise up and poison education, but the sensible people always assume it’s going to be fine and that they don’t need to exert themselves.

New Zealand is looking better every day

I may have to think about retiring in 15 years or so, and I may just have to move to New Zealand. The trends are all going in the right direction.

There has been a sharp rise in the number of New Zealanders with no religious affiliation, new research shows.

In a study by the University, 40 per cent of respondents say they have no religious affiliation compared to 29 per cent 17 years ago.
Just over a third of New Zealanders describe themselves as religious.

Sounds so lovely. Of course, it’s not perfect yet:

Fifty-three per cent say they believe in God (although half of those say they have doubts), 20 per cent believe in some form of higher power and about third say they don’t believe or don’t know.

However, 60 per cent say they would prefer children to have religious education in state primary schools with strongest support for teaching about all faiths.

Get to it, Kiwis — you’ve got about a decade to improve those numbers. I’m sure you can do it.

The irony is so bad, I’m having seizures

The US Conference of Catholic Bishops has issued a stern warning (definitely including fingerwagging, with possibility of ruler rapping) against the heathen practice of Reiki.

To use Reiki is to operate “in the realm of superstition, the no-man’s-land that is neither faith nor science,” the bishops warned, urging Catholic healthcare institutions, retreats and chaplains to ditch the therapy, which originated in Japan in the 1800s.

No, stop! I’m twitching so badly, I think I’ve damaged something.

Maybe I need some healing at Lourdes…

It’s Springtime for Molly on Pharyngula

I noticed that, in this recent thread asking why you were all here, that many of you said it was for the community and for the smart commenters here. Nobody said it was for my irresistible physical beauty and scintillating and delicate charm…in fact, I got the distinct impression I could drop dead and you’d all keep chatting away happily. Well, then, I guess it’s time to update the Molly awards, since you all love each other so much. <sniffle>

The people have spoken, and they have selected the lovely and diplomatic raconteur, Sven DeMilo, as the recipient of the Molly for the month of February. Kudos! Speech! No, never mind, sit down again. You’re old news now.

Now you have to look back to the past month and pick another worthy recipient for the month of March — simply leave a comment here saying who was your recent favorite, and why. Special note: I’m going to have to specifically exclude the recent outcasts from Survivor: Pharyngula! from eligibility, because I happen to know most of you are incorrigible smart-asses who would love to prank the voting with a certain name.

Guiyu oneiros

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

A fish is a fish, right? They’re just a blur of aquatic beasties that most people distinguish by flavor, rather than morphology or descent. But fish are incredibly diverse, far more diverse than terrestrial vertebrates, and there are significant divisions within the group. Most people know of one big distinction, between the Chondrichthyes (fish with cartilaginous skeletons, like sharks and rays) and the Osteichthyes (fish with bony skeletons), but there’s another particularly interesting split within the Osteichthyes: the distinction between Sarcopterygians (the word means “fleshy fins”, and we call them lobe-finned fishes colloquially) and the Actinopterygians, the ray-finned fishes. The lobe-finned fishes most distinctive feature is the muscular and bony central core of their fins — extant forms are the coelacanth and lungfish. It is this lineage that led to us terrestrial tetrapods, but other than that successful invasion of the land, the sarcops were something of an aquatic failure, with only a few genera surviving. The ray-finned fishes, on the other hand, are a major success story, with more than 28,000 species today. To put that in context, there are only about 5,500 species of mammals.

The Sarcopterygii and the Actinopterygii must have begun diverging a long time ago, and a couple of questions of interest are a) when did the last common ancestor of both groups live, and b) what did it look like? We don’t have a good and specific answer yet, because Osteichthyes origins are lost far, far back in time, over 400 million years ago, but every new discovery edges us a little closer. What we now have is a well-preserved fossil of a fish that has been determined to be an early sarcopterygian, and it tells us that a) the last common ancestor had to have lived over 419 million years ago, the age of this fossil, and the divergence probably occurred deep in the Silurian, and b) this animal has a mosaic of primitive Osteichthyan features, which tells us that that last common ancestor may well have shared some of these elements. It is another transitional fossil that reveals much about the gradual separation of two great vertebrate groups.

And here it is:

i-ba4ab7bcea24c3417d69b43fa74705c5-guiyu.jpeg
(Click for larger image)

a, b, A near-complete fish in part and counterpart. c, Close-up view of the anterior portion of the trunk shield in dorsal view, showing MD1 and MD2 flanked by rhomboid scales. d, Close-up view of the dorsal fin spine. MD1, first median dorsal plate; MD2, second median dorsal plate. Scale bar, 1 cm.

That may be a bit disappointing at first — it looks like Silurian road-kill — but really, that’s a remarkable good and useful specimen. The animal was covered with thick bony scales, and the skull was built of thick bony plates, and so while it was squashed flat by pitiless geology, the pieces are all there, and it can be reassembled into a much more fishy state. This drawing may be more satisfying:

i-79484c5905eacb406749c6e61d25ddb4-guiyu_resto.jpeg
(Click for larger image)

a, Restoration of the entire fish in lateral view. b, Interpretive drawing of the holotype V15541. Areas shaded in grey are unknown, and are reconstructed from other early osteichthyans. ano, anterior nostril; br, branchiostegal ray; cla, clavicle; cle, cleithrum; drs, dorsal ridge scale; dsp, dorsal fin spine; et, extratemporal; eta, accessory extratemporal; f.add, adductor fossa; f.gl, glenoid fossa; gu, gular; ju, jugal; l.ext, lateral extrascapular; lj, lower jaw; m.ext, median extrascapular; mx, maxillary; n.sp., spiracular notch; op, opercular; pa, parietal shield; pcl, postcleithrum; pop, preopercular; ppa, postparietal shield; psc, presupracleithrum; pt, post-temporal; scl, supracleithrum; sop, subopercular; sp., pectoral spine; tr, lepidotrichia; vrs, ventral ridge scale.

Now it looks like a kind of armored, spiky salmon with a thick muscular body (and yes, I too wonder about flavor, and would like to taste a slab of that). It’s definitely not a salmon, though — the bony structure is a curious set of compromises where some features are distinctly sarcopterygian, some look like they belong on a primitive actinopterygian, and others are unique or show affinities to characters of ancient extinct fishes, like rhipidistians. This is very cool. What we see here are relics of an ancient common osteichthyan ancestor, which are being honed into the specific characteristics of the Sarcopterygii. The analysis of the totality of the animal’s features, though, place it more in the lobe-finned than the ray-finned clade. That places it on a branch of the line leading to us…a very, very old branch, making this your many-times-great grand uncle, or cousin only a few million times removed. Now my curiosity about a taste-test is making me feel mildly cannibalistic.

i-d888d1f84f126c55eb104f249de00adb-guiyu_phylo.jpeg
(Click for larger image)

The topology is the most parsimonious tree arising from a matrix of 23 taxa coded for 153 morphological characters (tree length = 292, consistency index = 0.572, retention index = 0.737, rescaled consistency index = 0.421). The numbers at nodes indicate bootstrap support (where the value is greater than 50%) and Bremer decay index (bottom and top numbers, respectively). Eif., Eifelian; Ems., Emsian; Fam., Famennian; Fras., Frasnian; Giv., Givetian; Gor., Gorstian; Loch., Lochkovian; Lud., Ludfordian; Prag., Pragian.

When you look at that diagram, what should jump out at you is all the diversity in the Devonian, the so-called Age of Fishes, and the paucity of representative fossils from the Silurian…which is exactly where all the interesting branch points in the fish family tree are located. Once again, paleontology is a predictive science, and this tells us where to look for the next batch of exciting and informative fossils.


Zhu M, Zhao W, Jia L, Lu J, Qiao T, Qu Q (2009) The oldest articulated osteichthyan reveals mosaic gnathostome characters. Nature 458:469-474.