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.

Ben Carson did experiments on tissue from aborted fetuses

madsci

The paper leaves no room for ambiguity.

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Note that there’s nothing at all wrong with this — the use of fetal tissue in these kinds of experiments, and many more, is ubiquitous, and it is not obtained by magic, but by the ethical donation of fetal material from abortions and miscarriages and stillbirths. I don’t object at all to Carson having participated in this kind of research.

I do object to him now declaring that it is unethical in all circumstances.

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Botanical Wednesday: I need!

We’re leaving for the West coast on Friday, and of course my creaky old joints are lancing me with stabby excruciating pain. I have seen my doctor. I have pills. Because I must restore myself with red cedar, Sitka spruce, sea stacks, tide pools, banana slugs, great herds of sea urchins, and the ocean and the mountains, I will get there if Mary has to carry me on her back.

The Olympic National Forest is also where Mary and I had our honeymoon, 35 years ago. If ever I could just ditch all my responsibilities and retreat somewhere to avoid everything, this is where I’d go. But don’t bother looking for me. Just be satisfied with the news that, if I vanish, sightings of hairy ape-like creatures in the wilderness of Washington state will spike.

Christians can get awfully reductionist when it suits them

elephant-embryo

Amanda Marcotte rips into stupid gotcha by Marco Rubio.

When Rubio appeared on CNN after Thursday night’s Republican debate, he kept insisting that this vague entity called “science” has declared that human life begins at conception. (Actual biologists, for what it’s worth, argue that life is continuous and that a fertilized egg is no more or less alive than a sperm or an unfertilized egg.) CNN host Chris Cuomo vainly tried to point out that “science” says no such thing, and Rubio got a little excited.

“Let me interrupt you. Science has—absolutely it has. Science has decided… Science has concluded that—absolutely it has. What else can it be?” he asked. Then Rubio reared up for what he clearly intended as his wowza line: “It cannot turn into an animal. It can’t turn into a donkey. The only thing that that can become is a human being.”

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Those sneaky gingers pop up everywhere

gingers

I have a brother with red hair. I also have a son with red hair. Once upon a time, my beard and mustache contained many red hairs among the dominant browns. If you’ve ever wondered how these gingers appear all over the place, Petra Haak-Bloem offers a good explanation (although it needs some editing: how many different ways can they spell pheomelanin?).

The shade of hair color is determined by the amount of melanin, or pigment, in the hair. Your DNA not only encodes what kind of pigment you have, but also how much of it. “For white people the shades are dependent on two sorts of melanin: eumelanine (black pigment) and pheomelanine (red pigment). Hair cells of dark haired people only contain eumelanine. Blondes have less eumelanine. And redheads’ hair contains mostly pheomelanine,” Haak-Bloem says.

“More than a decade ago, researchers discovered that one gene (MC1R) on chromosome 16 plays an important part in giving people red hair. MC1R’s task is making a protein called melanocortin 1. That proteine plays an important part in converting pheolmelanine into eumelanine,” Haak-Bloem tells me. “When someone inherits two mutated versions of the MC1R-gene (one from each parent), less pheomelanine is converted into eumelanine. The feomelanine accumulates in the pigment cells and the person ends up with red hair and fair skin.”

The unexpectedly red beard is the effect of the same mutation in the MC1R gene. When you only have one mutated MC1R, red hair can appear in (unwanted) places. But even Haak-Bloem wasn’t completely sure of the mechanism. Having a deviant red beard has never been linked to any deadly diseases, so it’s pretty low on the research priorities list.

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