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.

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The first comment on any of the lefty blogs is usually 'Frist' or 'Fitz'. What is it here - Darwin! or PZ!

Uh, usually we comment on the post itself.

PZ, I thought you might like to see the frankly hilarious evolution/creationism debate going on on facebook. A group has formed acrewing over ½ million members. Someone started what was initially obviously flamebait but if you want to see the new bright future for the US going round in circles with more than half of it going "God did it" you're welcome to! Within 12 hours it grew to 3000 posts.
Its on the "Students against Facebook News Feed (Official Petition to Facebook)" group, the thread's called "Creationists suck".
The following URL might work for you, I'm not sure.
http://nottinghamac.facebook.com/topic.php?uid=2208288769&topic=3814

If we have to choose just one, I wonder if Loligo might not be a bad choice. And it is just one of several cephalopods that are or have been raised in lab facitilies in Galveston, Texas, my old stomping grounds. The Loligo are lovely!

From http://www.utmb.edu/nrcc/OnSiteFacil.htm : "Three local squid species are available- Lolliguncula brevis, Loligo plei and Loligo pealei. The squid Sepioteuthis lessoniana and the cuttlefishes Sepia officinalis and Sepia pharaonis are cultured year-round. Wild-caught chambered nautilus, Nautilus pompilius, are maintained year-round or as needed. Thus, all sizes and developmental stages of cephalopods are available. Cells, tissues and organ systems can be prepared in our laboratories. Archived squid and octopus samples of known age are also available."

By ctenotrish, FCD, PhD (not verified) on 07 Sep 2006 #permalink

The rate of genome sequencing is going to increase quite considerably over the next year or so, so I'm sure we'll be seeing one within a few years.

Here's a Euprymna cDNA project...
Chun et al., An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri. BMC Genomics. 2006 Jun 16;7(1):154

If a mollusc (Aplysia)is already being done, then for a cephalopod is there really much added value, in terms of understanding their brain development and evolution, in doing a whole-genome rather than just expressed genome approach? Though as Chris said, the day is fast approaching when doing the whole genome of just about anything anyone wants will be quite feasible.

By Steve LaBonne (not verified) on 07 Sep 2006 #permalink

A specific "God spot" was recently ruled out for the vertebrate representatives (er, humans).

It'll be interesting to see if the cephalopod brain will be shown to harbor an identifiable "FSM spot."

By Steviepinhead (not verified) on 07 Sep 2006 #permalink

As fond as I am of our ASPM paper (and wish I'd been reading Pharyngula when it came out), I like the Cell paper better for demonstrating a broader trend (although I objected then and now to a lot of the overblown language that made it into the paper).

I, for one, welcome our cephalapod genome project. Evolutionary genomics can be unfortunately hidebound about comparisons. The rodent as outgroup is standard by virtue of the mouse and rat genomes having been available for so long, and there's a strange "a primate is a primate is a primate unless it's a chimpanzee" attitude that can be less than helpful. And the FSM forbid one should suggest that comparisons with multiple non-mammalian genomes would be informative.

Yes, join the Facebook group. The news feed is dumb.

And I think this post wins the award for Most Categories.

Have they actually got viable DNA samples for those big buggers whales feed on?

It'd be interesting to see how they evolved...

By Phoenician in … (not verified) on 07 Sep 2006 #permalink

Best brain-genetics analysis is from molecular genetics professor Johnjoe McFadden (p. 313, Quantum Evolution: How Physics' Weirdest Theory Explains Life's Biggest Mystery, W.W. Norton, 2002):

"If, instead, the voltage gate absorbing the photon is in a neurone committed to firing (thousands of gates already open), the absorption event will similarly make no macroscopic difference to the cell or to the brain (since the neurone will fire anyway) and the interaction may once again remain quantum. However, now imagine that the channel is critical in a neurone poised on the brink of an action potential. The superposition ({photon absorbed and channel open (+/-) photon not absorbed and channel closed}) will now become a larger entanglement: {photon absorbed and channel open and neurone fired (+/-) photon not absorbed and channel closed and neurone not fired}. The channel's alternative states (open or closed) will be associated with very different fates for the neurone: firing or not firing. This quantum event will now make a difference to the neurone, the brain, and potentially, the life of the brain's owner. Under these circumstances (of maximum environmental entanglement), decoherence will be instantaneous. At this point the photon, as a quantum component of the Cem-field [Consciousness em field], must make a choice -- to be absorbed or not -- and a quantum measurement will be made."

Believe or not, NHGRI (the National Human Genome Research Insitute), does take requests for sequencing other organisms that might be useful for comparative genomics. They've done chickens, why not cephalopods?

Why don't you write to them and propose a cephalopod genome project?

You haven't ticked Francis Collins off that much have you? ; )

In all fairness, we don`t have the capacities to cover everyone`s wishes to cover each and every organism that one is interested to study.

Doing a Euprymna is beyond reason and significance at the given time and i am sure we both know that. I am aware about PZ`s fascination for prolly the whole class of marine animals.

But the descissions which animals are next to sequence comes down to the scientific community and which animal raises the most questions. Given my own specialization in neurobiology, the sequencing of Aplysia is not only a must it is already way delayed.

Besides the sequencing of the microbial world is the most influential and paramount for the future. If keeps track of technology in DNA sequencing then it is foreseeable that whole genome sequencing will be forseeable. As for other animals whole genome shotgun sequencing suffices to study them in an evolutionary context - something that would have never sufficed for the human genome project and other mammalia due to their satellites - and Craig knows that just as well, given that he ain`t stupid just too proud to admit it.

If you wanna sequence them then use your readership. Ask for donations and start out little by little. You don`t need the whole genome but only the ones that really interest you. A few used sequencers will suffice. Nowhere are they easier and cheaper to get than in the US. SO SHOW SOME INITIATIVE DUDE!!

I and many other scientists have no interest in your favorite mollusc, if that means cutting down on other way more important organisms which have been in the queue for years.

So i don`t even get your post unless you wanna show that you ponder about doing some sequencing on your own. These day`s its so easy that all you would need is two undergrads and train them for two days how to purify cut align and use the sofware and maintain the sequencer (just give `em the manual ).

Besides if you wanna raise interst in a whole genome approach (which you won`t be able to do on your own - duh!) you first gotta show the significance to push them not only forward but actually into the overbooked sequencing schedule.

Oh and btw: apparently there is already something in progress: http://www.squidblog.net/2005/10/26/the-squid-genome-project/

Biology is exciting, it gives me a lot of aha! moments.

Speaking of cognition and evolution, today I already got my fill with 3 aha! moments from http://www.sciencedaily.com/releases/2006/09/060908000933.htm .

They describe comparative psychological research - looking at species cognition along the phylogenetic tree was the first aha! The second aha! was that animals have two main search strategies, features or location. This is one of the recurring tasks I do well, so I've never taken the effort to model how it's done. And the third aha! is the result that human development reassess the default evolutionary preference as early as 3 years, switching from locationbased to featurebased preference.

This makes me expectant to see what the cephalopod comparison will turn up.

By Torbjörn Larsson (not verified) on 08 Sep 2006 #permalink

There's real work to be done before a cephalopod genome project will happen. You need to have a cephalopod:

* with proven utility as a model organism

* for which preliminary work on its genome has already been done, such as determining the molecular weight (a good stand-in for genome size, see ) and some estimation of how repetitive it might be
www.genomesize.com has estimations for some Octopus and squid (Euprymna and Loligo) species.

* with well-established research strains and breeding colonies, or at least long-lived individuals (can inbred strains be developed to simplify sequencing?)
-- For example, the individual sea urchin Strongylocentrotus purpuratus that was sequenced was not captive-bred, but urchins are long-lived and that individual has provided sperm for DNA samples over several decades.
-- Honeybees cannot be deeply inbred without diminishing hive viability due to diploid males, but at least normal haploid drones, which develop from unfertilized eggs, can be sequenced to sample the genome of the queen, which may live for several years.
-- http://www.ncrr.nih.gov/ncrrprog/cmpdir/INVERT.asp cites a cephalopod center in Galveston with Sepioteuthis (squid) and Sepia (cuttlefish) lab-cultured populations.

So, a start would be to get a group of cephalopod researchers united behind a common model organism, either one of those already cultured or a new one, and get some initial results before writing up a white paper to NHGRI. More information about proposing a genome project is at http://www.genome.gov/11007951, and a list of those already approved is at http://www.genome.gov/10002154 (including the sea slug Aplysia and the freshwater snail Biomphalaria -- the links are for the white papers proposing those genome projects).

Just clicking around the internet and found this site. Interesting to see that our little essay has provoked some debate. Thanks for reading. As to Paco's point that there is real work to be done before a cephalopod genome is sequenced, all good points. The only one I would argue with is the claim that one has to unite behind 'a common model organism', those days will be gone within a decade. The new ultra-high throughput sequencing strategies under development (motivated primarily by pharmacogenomics considerations- the pharma guys want to be able to sequence individual humans on a routine basis) should allow some deranged scientist to sequence his/her favourite calamari sooner than one might expect. I don't think it will be done by the current 'Manhattan Project' approach to genomes being run by the NHGRI, although I applaud them for their very important work and stimulus to technology development in the field.

I am not a great fan of blogs, but after reading some on the anti-creationist activities of PZ Myers I will try to find time to come back and read other sections.

thank you,

Mike Fainzilber

If a mollusc (Aplysia) is already being done, then for a cephalopod is there really much added value, in terms of understanding their brain development and evolution, in doing a whole-genome rather than just expressed genome approach?

IIRC, gastropods and cephalopods diverged in the Cambrian or before, so the differences in genome organisation etc. will not be trivial! one could rather ask why we are sequencing lots of redundant mammals ;)

Doing a Euprymna is beyond reason and significance at the given time and i am sure we both know that. I am aware about PZ`s fascination for prolly the whole class of marine animals.

Aplysia is a marine animal too, you know...

But the descissions which animals are next to sequence comes down to the scientific community and which animal raises the most questions. Given my own specialization in neurobiology, the sequencing of Aplysia is not only a must it is already way delayed.

Oh, boo hoo hoo. You can't seriously think that adding another mollusc in the sequencing queue would cause them to bump down Aplysia that is already being assembled? When they are considering sequencing 20 effing strongylid nematodes? Sequencing another mollusc would facilitate, not slow down Aplysia research (comparative genomics!).