Remember this on election day

Look back on Mitt Romney in 2011:

KING: You’ve been a chief executive of a state. I was just in Joplin, Missouri. I’ve been in Mississippi and Louisiana and Tennessee and other communities dealing with whether it’s the tornadoes, the flooding, and worse. FEMA is about to run out of money, and there are some people who say do it on a case-by-case basis and some people who say, you know, maybe we’re learning a lesson here that the states should take on more of this role. How do you deal with something like that?

ROMNEY: Absolutely. Every time you have an occasion to take something from the federal government and send it back to the states, that’s the right direction. And if you can go even further and send it back to the private sector, that’s even better.

Instead of thinking in the federal budget, what we should cut — we should ask ourselves the opposite question. What should we keep? We should take all of what we’re doing at the federal level and say, what are the things we’re doing that we don’t have to do? And those things we’ve got to stop doing, because we’re borrowing $1.6 trillion more this year than we’re taking in. We cannot…

KING: Including disaster relief, though?

ROMNEY: We cannot — we cannot afford to do those things without jeopardizing the future for our kids. It is simply immoral, in my view, for us to continue to rack up larger and larger debts and pass them on to our kids, knowing full well that we’ll all be dead and gone before it’s paid off. It makes no sense at all.

You know he’s not going to do a thing to slow the advance of global climate change (or does he think that can be done at the level of individual states, too?), and he doesn’t support federal emergency services. Why should he? Disasters like this don’t discomfit the rich.

The CephSeq Consortium has a strategy

I approve this plan. A number of researchers have gotten together and worked out a grand strategy for sequencing the genomes of a collection of cephalopods. This involves surveying the phylogeny of cephalopods and trying to pick species to sample that adequately cover the diversity of the group, while also selecting model species that have found utility in a number of research areas — two criteria that are often in conflict with one another. Fortunately, the authors seemed to have found a set that satisfies both (although it would have been nice to see the Spirulida and Vampyromorpha make the cut — next round!). Here’s the initial group, table taken directly from the text with the addition of a few pretty pictures for those of you unfamiliar with the Latin names.

Table 1: Cephalopod species proposed for initial sequencing efforts.

Species Estimated genome size Current sequencing coverage Geographic distribution Lifestyle juvenile/adult Research importance
O. vulgaris 2.5-5 Gb 46× world-wide planktonic/ benthic classic model for brain and behavior, fisheries science
O. bimaculoides 3.2 Gb 50× California, Mexico benthic emerging model for development and behavior, fisheries science
H. maculosa 4.5 Gb 10× Indo-Pacific benthic toxicity
S. officinalis 4.5 Gb - East Atlantic- Mediterranean nectobenthic classic model for behavior and development, fisheries science
L. pealeii 2.7 Gb - Northwest Atlantic nectonic cellular neurobiology, fisheries science
E. scolopes 3.7 Gb - Hawaii nectobenthic animal-bacterial symbiosis, model for development
I. paradoxus 2.1 Gb 80× Japan nectobenthic model for development, small genome size
I. notoides - 50× Australia nectobenthic model for development, small genome size
A. dux 4.5 Gb 60× world-wide nectonic largest body size
N. pompilius 2.8-4.2 Gb 10× Indo-Pacific nectonic “living fossil”, outgroup to coleoid cephalopods

It’s a nice balance. There’s a pair of related octopus (Octopus vulgaris and Octopus bimaculoides) and a pair of related squid (Idiosepius paradoxus and Idiosepius notoides) so common features to each group can be recognized, a couple of model organisms used in neuroscience (Loligo pealeii) and developmental biology (Euprymna scolopes), and a couple of just plain cool animals, the blue-ringed octopus (Hapalochlaena maculosa) and the giant squid (Architeuthis dux). And of course you have to include a cuttlefish (also an important research model), and a nautilus for the outgroup.

It’s going to be challenging — cephalopods are like us in having large, sloppy genomes with lots of repeats and accumulated junk.

Like all good science, too, this is going to be open and accessible.

We therefore propose to adopt a liberal opt-in data sharing policy, modeled in part on the JGI data usage policy, which will support the rapid sharing of sequence data, subject to significant restrictions on certain types of usage. Community members will be encouraged to submit their data, but not required to do so. We plan to provide incentives for this private data sharing by (1) developing a community data and analysis site with a simple set of automated analyses such as contig assembly and RNAseq transcript assembly; (2) offering pre-computed analyses such as homology search across the entire database; and (3) supporting simple investigative analyses such as BLAST and HMMER. We also plan to provide bulk download services in support of analysis and re-analysis of the entire dataset upon mutual agreement between the requesting scientist and the CephSeq Consortium Steering Committee (see below), who will represent the depositing scientists. Collectively, these policies would provide for community engagement and participation with the CephSeq Consortium while protecting the interests of individual contributors, both scientifically and with respect to the Convention on Biological Diversity. Policy details will need to be specified and implementation is subject to funding. Our intent is to build an international community by putting the fewest barriers between the data and potential researchers, while still protecting the data generators.

I also like that there’s an appreciation of the importance of wider communication of this information beyond the sphere of nerdy genomics researchers and obsessed cephalofreaks. The authors recognize that cephalopods are important barometers of climate change and the ocean environment, and that people are just plain fascinated with them.

People are fascinated by cephalopods, from Nautilus to the octopus to the giant squid. The coupling of genomics to cephalopod biology represents a fusion of two areas of great interest and excitement for the public. This fusion presents a tremendous educational platform, particularly for K-12 students, who can be engaged in the classroom and through the public media. Public outreach about cephalopod genomics will help build support for basic scientific research, including study of marine fauna and ecology, and will add to the public’s understanding of global changes in the biosphere.

Unfortunately, this short paper is a little thin on details of particular interest to me: “Education and outreach will be emphasized for broad dissemination of progress in cephalopod genomics at multiple levels, including K-12, undergraduate and graduate students, and the public at large.” I’d be curious to see more about the how of doing that, but I’m glad it’s on their list of priorities. Part of their plan is building a website, but unfortunately when I just checked it wasn’t yet available.


Albertin CB, Bonnaud L, Brown CT, et al. (2012) Cephalopod genomics: A plan of strategies and organization. Stand Genomic Sci 7:1.

Fair warning to convention attendees

So I just got back from CSICon, which was great fun. I gave a talk on the role of chance in evolution (it’s more important than many think), and I think people recorded it. I also have a rough summary that I’ll polish up and post to Pharyngula. But…

You’ll have to wait a bit. This year I’ve decided I can no longer drive myself into total mental collapse by doing new talks all over the place, so I’m going to be recycling a fair bit. I’m going to use this same talk at Skepticon and Eschaton 2012, so if you’re going to those events too, you might want to skip one of my sessions. Except that at CSICon, I had to compress it down to a half hour, so there will be some additional stuff at those two meetings.

I’m also scheduled to do two talks at Eschaton, so I’m not going to give that same talk twice. It’ll be a talk on science education on Saturday morning, and one on evolutionary theory on Saturday evening.

And then in December I’ll post a written summary of my talk, and try to come up with something new to say for Spring meetings.

Ignore that presidential campaign over there

I don’t like Obama.

There. I said it. I think he’ll go down in history as a mediocre president — not a bad one, just one who didn’t change a flawed system at all, who was so focused on being moderate and compromising that there was no hope of any significant change. I also think his foreign policy is bloody-handed and disastrous, and if you’re interested in church-state separation and secular government, I’m sorry, but he’s had you all fooled. He’s not a closet atheist, but quite the opposite.

But next week, I’m going to go into the voting both and punch that ballot next to Obama’s name.

I’m not happy about it.

Here’s the problem: we’ve all been played. All of the focus is on the presidential election, in a winner-take-all two party system. And the presidential election is a distraction. It’s been reduced to a numbers game, a horse race where policies don’t matter, and all you have left to do is to pick one out of two. All the work has been done before you enter the voting booth, and that work is aimed at limiting your choices. So this time around, your choice is the evangelical Christian who brags about killing terrorists while making incremental improvements to the economy, or the Mormon robot who’s going to serve as a slave to the bankers and merchants of greed who destroy the economy, or nothing. So you try to pick the lesser of two evils.

I know what people will say. You have to vote on your principles, or nothing will change. When I just look at the issues, I agree: I ought to vote for Jill Stein, whose stand on just about everything agrees with mine. (Don’t tell me about Gary Johnson — I look at his positions and see a selfish moron who’d be worse than Romney). But Jill Stein isn’t going to win, and my vote would be thrown away, and worse, Jill Stein is throwing away her time and effort in a quixotic race that has already been decided. It will be one of two. The two are fixed. Third party candidates are a snare and an illusion.

I’m not saying that we’re doomed, though, just that the presidential race is the wrong place to effect change.

The right place is everywhere else. Maybe the primary campaigns would be better: we need to get candidates in place that don’t require us to hold our noses in order to vote for them. The Republican field is always a race to find the one candidate just crazy enough to satisfy a badly deranged base, while not so obviously crazy as to alienate everyone else, so forget them. The Democrats always seem to be looking for the moderate who won’t really change the system (that would be scary) and who will inspire just enough to squeak into office…but not inspire so much that people will wake up to our problems. I suspect that both parties will fundamentally resist change.

So maybe that’s not even the best place to work on fixing the election system. Especially in this election, the power of incumbency is so great that no one was even going to look seriously at an alternative to Obama.

You know where the elections really matter, where you really have a choice? At the local level. The Green Party is stupid to throw so much effort into a presidential campaign right now — they ought to be focused on building a base. I would vote for a Green for city council or district representative in a heartbeat. And once they’ve built a deep party structure, they become serious candidates for higher office, because they will have the backing of people doing good work on the ground.

This is the same advice we give to people fighting creationism. Run for local school boards, because that’s where you can make a difference. Our opponents know that; these small offices are packed with ideologically conservative Christians who can have an effect far greater than their numbers should allow. While you’re focused on who is running for president, they’ve placed a team of cretins on local government to stymie any progressive, rational efforts towards bettering the country.

Stein has served two terms as a town meeting representative in Lexington, Massachusetts, which is a good start. But we’d have been better served if she’d then moved up to a county or district office, instead of leaping for governor (failed) or president (doomed). She ran for the house of representatives, once, and lost…I’d rather she tried for that again. And I’d rather see Green Party candidates appearing all over the place, on zoning boards and city councils and school boards, rather than gambling on presidencies and governorships where they’ll preside over an army of Democrats and Republicans who’ll feel no loyalty at all to them.

So ignore the presidential campaign. We know we’re going to be stuck with the lesser of two evils, so just get it done. But what we people need to do next, and what we can do in this election, is vote everywhere else for third party candidates who better fit your values, and most importantly, donate and campaign for those candidates. Personally, I know that in the future my political donations (they aren’t much, I’m not a wealthy guy, so I’ll be realistic) will be aimed towards parties other than the Democrats. Any Greens looking for local office? Labor? Socialists? You can have my pennies. Democrats? Not until you acquire the vision to nominate real liberals and progressives. Until you stand for something other than not-Republican.

I’m home!

I made it back, scudding ahead of the oncoming hurricane! Actually, I saw no sign of it: everything was calm when I left Tennessee and North Carolina this morning, and all my flights were on time. I know some of the east coast people were seeing flight cancellations, but I think my timing was just right to be well ahead of it all.

I hope it all dribbles away quickly, but otherwise, best of luck to those staring Sandy’s landfall in the face…and better yet, best of preparation.