IDiots, suckers, and the octopus genome

The genome of the small octopus, Octopus bimaculoides has recently been sequenced. The results are reported in Nature (Albertin et al., 2015).

The octopus is a cephalopod along with squid and cuttlefish. These groups diverged about 270 million years ago making them more distantly related than humans and platypus. As expected, the octopus genome is similar to other mollusc genomes but also shows some special derived features. Some gene families have been expanded—a feature often found in other genomes.

In gene family content, domain architecture and exon–intron structure, the octopus genome broadly resembles that of the limpet Lottia gigantea, the polychaete annelid Capitella teleta and the cephalochordate Branchiostoma floridae. Relative to these invertebrate bilaterians, we found a fairly standard set of developmentally important transcription factors and signalling pathway genes, suggesting that the evolution of the cephalopod body plan did not require extreme expansions of these ‘toolkit’ genes. However, statistical analysis of protein domain distributions across animal genomes did identify several notable gene family expansions in octopus, including protocadherins, C2H2 zinc-finger proteins (C2H2 ZNFs), interleukin-17-like genes (IL17-like), G-protein-coupled receptors (GPCRs), chitinases and sialins.

Some of the expansion in these gene families may be due to specialized cephalopod features like large brains and nervous systems (protocadherins) and suckers on the tentacles (nicotinic acetylcholine receptor-like proteins).

Big brains and lots of suckers make it easy to tell an octopus from a clam.

The octopus genome is about the size of the human genome and 45% of the sequence is repetitive elements, mostly defective transposons—as in mammalian genomes. There are 33,638 predicted protein-coding genes but we can anticipate that this number will drop if enough effort is spent on annotation. The software used to predict genes is prone to false positives because it's better than having too many false negatives.

As expected, there are hundreds of genes that are unique in the octopus lineage or the coleoid cephalopod lineage. Some of the octopus-specific orphan genes will undoubtedly be false predictions since this is the common fate of many presumed orphan genes.

Our analyses found hundreds of coleoid- and octopus-specific genes, many of which were expressed in tissues containing novel structures, including the chromatophore-laden skin, the suckers and the nervous system. Taken together, these novel genes, the expansion of C2H2 ZNFs, genome rearrangements, and extensive transposable element activity yield a new landscape for both trans- and cis-regulatory elements in the octopus genome, resulting in changes in an otherwise ‘typical’ lophotrochozoan gene complement that contributed to the evolution of cephalopod neural complexity and morphological innovations.

There's nothing special here, folks. It's just a another genome that fits into the pattern seen with all other genomes.

Wait a minute ... the Intelligent Design Creationists have a different perspective. One of the leading IDiots, Casey Luskin, has this to say in "The Octopus Genome: Not "Alien" but Still a Big Problem for Darwinism" ...

These days, new genomes of different types of organisms are being sequenced and published on a regular basis. When some new genome is sequenced, evolutionary biologists expect that it will be highly similar to the genomes of other organisms that are assumed to be closely related.

As ENV already noted, the latest organism to have its genome sequenced has confounded that expectation: the octopus, whose genome was recently reported in Nature. It turns out to be so unlike other mollusks and other invertebrates that it's being called "alien" by the scientists who worked on that project ...

Obviously no one thinks the octopus is an "alien" from another planet. (Nature News quotes one co-author of the paper on the genome noting that the alien quip is a "joke.") But it certainly is alien to standard evolutionary expectations that genomes of related species ought to be highly similar. Thus, Nature points out the large number of unique genes found in the octopus genome:

I think Casey Luskin is relying far too much on a popular press release rather than actually reading the paper.

He made the same point a few days ago in his first post on the octopus genome [Octopus Genome Defies Evolutionary Expectations]. Instead of looking at the big picture, which shows that the octopus genome is pretty much what is expected from its evolutionary history, Luskin focuses on the "unique" genes (orphans).

"Evolution of novel genes" --? Isn't that the question at hand? Where do novel genes come from? They found "a suite of octopus- and cephalopod-specific genes" that seem to have appeared out of nowhere. As for mechanisms that "can drive genomic novelty," their list does little more than assume that making more of existing things and shuffling them around will create novel things that do something useful. Try that with a copy machine, a book, and scissors.

Apparently this is a devastating blow to "Darwinism" and proof that gods specifically designed genes for suckers.

The IDiot crowd has been fixated on orphan genes for quite a few years now. I guess they've come to the realization that 99% of the genes in a typical animal genome look like they've evolved by standard evolutionary mechanisms. That leaves just a few genes that are unique to a particular species and have no recognizable ancestors. I guess these are the ones that indicate the presence of an intelligent designer and refute evolution.

The octopus genome isn't special since all species have some orphan genes—even after extensive annotation. Little facts like those don't stop the IDiots from sensationalizing the results of every new genome sequence.

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