Monday, August 24, 2015

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.


  1. "Little facts like those don't stop the IDiots from sensationalizing the results of every new genome sequence."

    Indeed. Without their "this new finding is a major problem for Darwinism" spin, they would have no reason to post about the the genome in the first place. It's not as if they are writing for an audience that is interested in learning science, so the spin is the whole point!

  2. Sorry, I'm new to this genetics thing, so may I ask: Where do "orphan" genes come from? They are the genes that are organism-specific & distinguish that organism from even its nearest relatives. Casey thinks they actually do, as it were, come out of nowhere. In fact, they come out of "somewhere". What's the somewhere?

    1. Work in ants reveals that some orphan genes come from non-coding DNA that acquires a promoter. There are other sources:

      "Some can be traced to highly divergent products of gene duplications, overlapping or anti-sense reading frames (overprinting), domesticated transposons, resurrected
      pseudogenes, or early frameshift mutations [citations]. Others may arise de novo from non-coding sequence."

      -- Arendsee et al. 2014,

    2. Eric,

      Here is a nice review of the topic of orphan gene evolution:

    3. Long story short: they are the result of long periods of accumulating mutations in already existing genomic sequences.

      They don't pop "out of nowhere".

    4. Twenty years ago I would have said that its absolutely impossible for a randomly chosen sequence to be transcribed and translated into a functional protein but it seems to me there is fairly good evidence that its happened.
      If this turns out to be true we can forget all the other arguments made in the Evo ID debate. This makes them all superfluous. This observation alone would completely demolish the ID position, and we could all go home

    5. The Szostak lab found functional proteins (four different ones) in a pool of about 10^11 random sequence proteins (sequences that were 80 amino acids in length). And they only tested for one function (bind ATP), they could have tested for thousands of additional functions, such as chemical catalysts and binding to countless other molcules. They also only tested at one temperarure. Who's to say what else could be found in that pool of random sequence proteins?

    6. 1. Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

      Comparative genomic analyses have revealed that genes may arise from ancestrally nongenic sequence. However, the origin and spread of these de novo genes within populations remain obscure. We identified 142 segregating and 106 fixed testis-expressed de novo genes in a population sample of Drosophila melanogaster. These genes appear to derive primarily from ancestral intergenic, unexpressed open reading frames, with natural selection playing a significant role in their spread. These results reveal a heretofore unappreciated dynamism of gene content.

      2. Emergence of a New Gene from an Intergenic Region

      It is generally assumed that new genes would arise by gene duplication mechanisms, because the signals for regulation and transcript processing would be unlikely to evolve in parallel with a new gene function [1, 2] . We have identified here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5–3.5 million years in a large intergenic region. The region is present in many mammals, including humans, allowing us to exclude the involvement of gene duplication, transposable elements, or other genome rearrangements, which are typically found for other cases of newly evolved genes [3–8] . The gene has three exons, shows alternative splicing, and is specifically expressed in postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus and its emergence correlates with indel mutations in the 5′ regulatory region of the transcript. A recent selective sweep is associated with the transcript region in M. m. musculus populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and reduced testis weight. Our results show that cryptic signals for transcript regulation and processing exist in intergenic regions and can become the basis for the evolution of a new functional gene.

      Check Fig: 3 of the above paper. It shows how enabling mutations led to the emergence of this gene from non-coding DNA in the mouse lineage.

      3. Identification and evolution of the orphan genes in the domestic silkworm, Bombyx mori

      Orphan genes (OGs) which have no recognizable homology to any sequences in other species could contribute to the species specific adaptations. In this study, we identified 738 OGs in the silkworm genome. About 31% of the silkworm OGs is derived from transposable elements, and 5.1% of the silkworm OGs emerged from gene duplication followed by divergence of paralogs. Five de novo silkworm OGs originated from non-coding regions. Microarray data suggested that most of the silkworm OGs were expressed in limited tissues. RNA interference experiments suggested that five de novo OGs are not essential to the silkworm, implying that they may contribute to genetic redundancy or species-specific adaptation. Our results provide some new insights into the evolutionary significance of the silkworm OGs.

      Casey Luskin & Co. are 100% wrong. Orphan genes are not evidence for ID. They arise by the normal processes of mutation, selection etc and their ancestral sequences can be traced.

    7. All of which shows that the creationist position is sustained by their laziness to search and find. In an era pf easy access to information no less.

  3. There are bound to be some genes that fall outside the limit of the statistical techniques used to infer sequence homology. Luskin has no comment on the greatly superior number of genes with sequence similarity, except when he feels like saying "it's Common Design". So, orphan genes indicate genes that had to be designed from scratch, apparent homologs those that could be reused. It's all evidence of Design, heads I win tails you lose.

  4. For a non-technical introduction to where new genes come from, here's an article I wrote last year, and a TED-Ed video that emerged from it:

    1. Carl, that's a cool article but let's keep in mind that many of these so-called orphan genes have not been shown to have a function. They may be transcribed regions and they may produce some protein but that doesn't mean they are real genes with a confirmed biological function.

  5. Sometimes I think the biggest problem with science today is that press releases tend to be sensationalist. Journalists get confused, laymen get confused, and wicked people misuse every result possible.

    This is especially true for the life sciences and economics, since there are so many interests involved. How can we expect the general public to trust science like this?