I have returned to civilization

raven

And now I want to go back. It was a deeper journey into the wilderness than I expected — we left my brother’s house in Hoquiam and headed north, and after leaving wifi behind, we were a little surprised to learn we were also abandoning all of our cell phone carriers as well. We’ve been almost completely out of touch with the rest of the universe most of this week. We’d occasionally find a small trading post with slow, flakey wireless, and we’d fire off short Shackletonian missives to friends and family letting them know we still existed.

We also had slightly peculiar weather. It was lovely — fog and mist rolling in and softening the view everywhere.

driftwood

[Read more…]

A day in a time machine

kmroyals

I attended my 40 year high school reunion last night. It was interesting and strange. When I was a kid, we moved around a lot…but always within the Kent school district, which meant I attended most of the feeder elementary and junior high schools that funneled students into my high school, so I’d known some of these people since kindergarten. It’s not that I was particularly noticeable, since on top of being transient I was also the shy bookish type who didn’t speak up much, so I suspect most of them haven’t thought of me in decades. Then there was this giant gap when I left this area after graduation and didn’t come back, while many of my high school buddies stayed right here and kept in touch with each other.

I felt a bit space-alienish, wafting in from out of nowhere and encountering these strange old people, and after a moment of peering at each other’s faces (and our name tags), suddenly saying, “I remember you! We played tag at recess in 3rd grade!” Or the inevitable memorial slide show, and you learn about everybody who has died in the last 40 years, and you are ransacking your memory trying to place that person’s face, and there’s that warm glow when you remember that good day or that birthday party or that time in the bleachers when…and suddenly it sinks in that they’re dead. You just hoisted up that nice memory and now it’s never going to be anything more, and you’re not going to clink glasses with that old friend and reminisce about it, because they’re gone.

So it was all a little weird.

But mostly pleasant. I know many people have horrible memories of their school years, and all too often public schools are nightmarish mills of cliques and bullying and ugly social oppression, but I was lucky. I was the wimpy nerd, I would have been the easy target for bullying, but it didn’t really happen, and I had friends among all the little petty in-groups — the jocks, the cheerleaders, the stoners, the AV weirdos, everyone — and they were always pretty porous and accepting. Dang it, I don’t have any good horror stories to tell from those years! I went through high school without getting beat up (which, I know, is a low bar to set, but still…)

I think the thing is my high school class was generally just a decent group of people. I was lucky that way.

Now today Mary and I pile into the rental car and cruise west until we collide with OCEAN. We’ve got undisclosed locations stacked up along the coast of the Olympic Peninsula, and will be relaxing in splendid isolation.

My arrival in Seattle

Brain-Tumor

First thing when I landed at SeaTac: it started raining, as I’d hoped.

Second thing at the airport: we were taking a shuttle bus, and this guy started talking at his friend. I learned many things.

  • It’s obvious that cell phones cause cancer. They radiate energy. Energy causes cancer. QED.

  • The only reason we don’t have proof is that all us old guys use them sparingly. Just wait: a few more years, and all those kids going around with phones glued to their head will be getting brain cancer! Ha ha ha ha ha ha!

  • The best part: he got sort of quantitative. At low energies, they don’t cause cancer, but as the power goes up, the cancer-causing effects go up exponentially. Therefore, don’t use your cell phone when you got 4 or 5 bars! That’s when they’re most dangerous!

I’m imagining this guy wandering through life, using his cell phone to avoid places with “high energy radiofrequencies”, and refusing to take calls unless he’s got a perfect medium strength signal.

There is woo in Seattle, I can testify.

I repeat: Octopuses are NOT aliens

alienocto

Jebus. The stupidity of the media is maddening. Here are two articles now out there: Don’t freak out, but scientists think octopuses ‘might be aliens’ after DNA study and Octopuses ‘are aliens’, scientists decide after DNA study. These reporters are embarrassing.

Not to freak you out or anything, but scientists have just revealed that octopuses are so weird they’re basically aliens.

The first full genome sequence shows of that octopuses (NOT octopi) are totally different from all other animals – and their genome shows a striking level of complexity with 33,000 protein-coding genes identified, more than in a human.

Bullshit.

As I said earlier, the study is open access. Read it. If you can’t understand the big words and the details, then you shouldn’t be writing news stories on science.

The study says exactly the opposite. It shows that octopuses use genes shared with vertebrates — the common metazoan toolbox. They have amplified genes used by other earthly animal life in unique ways, but protocadherins are a known earthly family of molecules, and zinc finger genes are a known earthly family of genes. This study reinforces the concept of common ancestry.

Do I need to add that it’s even plainly said in the abstract? Just read the abstract!

The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians

I just know this nonsense is going to be propagated by creationists everywhere, and I’m going to have to slam it down repeatedly. The only good thing is that it’s an easy one to rebut, and I’ll have many excuses to wrap my virtual tentacles around their rhetorical throats and squeeze.


It begins.

Proving that octopuses are creatures that arrived from another planet, possibly from another solar system, may not be revealed any time soon. However, their alien existence upon the Earth is expected to be the focus of significant research in the coming years. It is likely that they will be found to be born of the Earth, but the mysticism that they may be aliens makes the genome discovery quite intriguing.

Friday Cephalopod: It’s not really an alien

a, Schematic of Octopus bimaculoides anatomy, highlighting the tissues sampled for transcriptome analysis: viscera (heart, kidney and hepatopancreas), yellow; gonads (ova or testes), peach; retina, orange; optic lobe (OL), maroon; supraesophageal brain (Supra), bright pink; subesophageal brain (Sub), light pink; posterior salivary gland (PSG), purple; axial nerve cord (ANC), red; suckers, grey; skin, mottled brown; stage 15 (St15) embryo, aquamarine. Skin sampled for transcriptome analysis included the eyespot, shown in light blue. b, C2H2 and protocadherin domain-containing gene families are expanded in octopus. Enriched Pfam domains were identified in lophotrochozoans (green) and molluscs (yellow), including O. bimaculoides (light blue). For a domain to be labelled as expanded in a group, at least 50% of its associated gene families need a corrected P value of 0.01 against the outgroup average. Some Pfams (for example, Cadherin and Cadherin_2) may occur in the same gene, however multiple domains in a given gene were counted only once. Bfl, Branchiostoma floridae; Cel, Caenorhabditis elegans; Cgi, Crassostrea gigas; Cte, Capitella teleta; Dme, Drosophila melanogaster; Dre, Danio rerio; Gga, Gallus gallus; Hsa, Homo sapiens; Hro, Helobdella robusta; Lch, Latimeria chalumnae; Lgi, Lottia gigantea; Mmu, Mus musculus; Obi, O. bimaculoides; Pfu, Pinctada fucata; Xtr, Xenopus tropicalis.

a, Schematic of Octopus bimaculoides anatomy, highlighting the tissues sampled for transcriptome analysis: viscera (heart, kidney and hepatopancreas), yellow; gonads (ova or testes), peach; retina, orange; optic lobe (OL), maroon; supraesophageal brain (Supra), bright pink; subesophageal brain (Sub), light pink; posterior salivary gland (PSG), purple; axial nerve cord (ANC), red; suckers, grey; skin, mottled brown; stage 15 (St15) embryo, aquamarine. Skin sampled for transcriptome analysis included the eyespot, shown in light blue. b, C2H2 and protocadherin domain-containing gene families are expanded in octopus. Enriched Pfam domains were identified in lophotrochozoans (green) and molluscs (yellow), including O. bimaculoides (light blue). For a domain to be labelled as expanded in a group, at least 50% of its associated gene families need a corrected P value of 0.01 against the outgroup average. Some Pfams (for example, Cadherin and Cadherin_2) may occur in the same gene, however multiple domains in a given gene were counted only once. Bfl, Branchiostoma floridae; Cel, Caenorhabditis elegans; Cgi, Crassostrea gigas; Cte, Capitella teleta; Dme, Drosophila melanogaster; Dre, Danio rerio; Gga, Gallus gallus; Hsa, Homo sapiens; Hro, Helobdella robusta; Lch, Latimeria chalumnae; Lgi, Lottia gigantea; Mmu, Mus musculus; Obi, O. bimaculoides; Pfu, Pinctada fucata; Xtr, Xenopus tropicalis.

Well, cool. We’ve got preliminary analysis of the octopus genome, and it’s full of tantalizing goodies, but it’s very preliminary, and the Nature news and comment left me unimpressed. One of the things they seemed to think was a big deal was that Octopus has more genes than we do.

Surprisingly, the octopus genome turned out to be almost as large as a human’s and to contain a greater number of protein-coding genes — some 33,000, compared with fewer than 25,000 in Homo sapiens.

But why would that be surprising? Humans aren’t the measure of all things, and we aren’t necessarily going to see any correlation between number of genes and complexity in multicellular organisms like people and octopuses. What is interesting in the paper, though, is how they achieved that greater number of genes. In vertebrates, what we see is the result of multiple rounds of whole genome duplication, followed by pruning away. There is no evidence of genome duplication at all in octopus; instead, select gene families underwent expansion. The two major families were protocadherins and a specific zinc finger gene group.

That’s interesting and suggestive! Protocadherins are important homophilic cell adhesion molecules mostly expressed in the developing nervous system — diverse protocadherins seem to be important in permitting more elaborate patterns of synaptic specificity. Vertebrates also have increased numbers of protocadherins, associated with greater neural complexity, and here we have an animal with the largest nervous system size among the invertebrates, and they too have a correlated increase in protocadherin number.

The zinc finger genes are transcription factors — they bind to DNA to regulate the expression of other genes. Octopus has 1800 different C2H2 ZNF genes! They are also a significant gene factor in humans, but we have only 500-700, and other molluscs have only a few hundred. These genes would permit greater and more complex developmental modulation.

You can see why a developmental biologist would find these differences provocative.

Another interesting difference is in the organization of the Hox genes. We have what is considered the approximately primitive condition, with the genes arranged in a tight cluster with colinear expression relative to the body plan — they are laid out in the same order on the genome as they will be expressed along the length of the body. I am not surprised at this result, however: the octopus Hox genes are scattered and fragmented, no longer arranged in a tidy linear array. The coleoid cephalopods have undergone some genuinely radical morphological transformations during evolution, so it is perhaps only to be expected that their genome shows some similarly radical rearrangements.

Go read the whole paper! It’s open access!

Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire. They have the largest nervous systems among the invertebrates and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system. To investigate the molecular bases of cephalopod brain and body innovations, we sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole-genome duplications in the octopus lineage. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc-finger transcription factors. Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described7, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.


Albertin AB, Simakov O, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, Brenner S, Ragsdale CW, Rokhsar DS (2015) The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature 524:220–224.

I am now officially on vacation

And you all know what that means, right? Cowards will try to sneak into the comments and leave asshole remarks, thinking they can get away with it. Just so you all know, while post frequency may diminish, I will be checking in every day, and kicking jerks out will be my prime priority. So if you try to take advantage of my distraction, all you’ll get is that I’ll be fucking pissed at you wasting my time, and the banhammer will be on a hair trigger.

So play nice, and use the report link on the left at anyone who tries to disrupt the flow of good conversation.