This could get interesting. I’ve seen a lot of stories about this recent paper on the tardigrade genome:

Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.

And here are a few of the follow-up stories in the popular press:

The Tardigrade, World’s Cutest Microscopic Animal, is Filled with Alien DNA

What the World’s Toughest Animal Is Really Made Of

Indestructible ‘Water Bears’ Have Really Weird Genomes

The authors are saying that about 18% of the tardigrade genome is a product of horizontal gene transfer…that they’re full of genes gathered up from bacteria, and that this was adaptive, playing a role in their ability to survive desiccation.

I have to say…I had my doubts. That seemed really unlikely, not only that they’d have a history of that much HGT, but that it could be assigned to functional roles. But OK, they published it, let’s see how it shakes out.

Here’s where it gets interesting: another paper has just come online that says it’s all an artifact. Tardigrades are tiny, on the order of a thousand cells, so it’s difficult to sample them for sequencing without also picking up lots of bacterial contamination. Here’s the abstract:

Tardigrades are meiofaunal ecdysozoans and are key to understanding the origins of Arthropoda. We present the genome of the tardigrade Hypsibius dujardini, assembled from Illumina paired and mate-pair data. While the raw data indicated extensive contamination with bacteria, presumably from the gut or surface of the animals, careful cleaning generated a clean tardigrade dataset for assembly. We also generated an expressed sequence tag dataset, a Sanger genome survey dataset and used these and Illumina RNA-Seq data for assembly validation and gene prediction. The genome assembly is ~130 Mb in span, has an N50 length of over 50 kb, and an N90 length of 6 kb. We predict 23,031 protein-coding genes in the genome, which is available in a dedicated genome browser at http://www.tardigrades.org. We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer. Additional analyses of the genome are ongoing.

And their conclusion:

Our assembly, and inferences from it, conflict with a recently published draft genome (UNC) for what is essentially the same strain of H. dujardini. Our assembly, despite having superior assembly statistics, is ~120 Mb shorter than the UNC assembly. Our genome size estimate from sequence assembly is congruent with the values we obtained by direct measurement. We find 15,000 fewer protein-coding genes, and a hugely reduced impact of predicted HGT on gene content in H. dujardini. These HGT candidates await detailed validation. While resolution of the conflict between these assemblies awaits detailed examination based on close scrutiny of the raw UNC data, our analyses suggest that the UNC assembly is compromised by sequences that derive from bacterial contaminants, and that the expanded genome span, additional genes, and HGT candidates are likely to be artefactual.

This could get very interesting.

I’m hearing occasional gasps of disbelief at the notion of a vegan Thanksgiving, so clearly I need to show you something to make you salivate.

That’s just an example — we’re having something different — but honestly, you can have a tremendous variety of textures and flavors, all delicious, without killing an animal.

Also not shown: Lefse is vegetarian, don’t you know.

At last, I understand human evolution. It’s all here in this painting.

Working from bottom to top, we witness the ascent of man. First, Homo erectus discovers fire, and stares at a burning twig. This was easier than it sounds, since all he had to do was light it from the volcano erupting over his left shoulder (there’s always a volcano, and it’s always erupting, in these things). If anyone has ever gone on a camping trip with those atavistic boy scouts, you will recognize his expression.

Next, Neandertals invent rocks. Two rocks at once…it’s a triumph!

The next big leap: men invent shaving and art. The subtle revelation in this image is that Cro-Magnon men were also all bronies — notice that he’s drawing a pony.

Civilization arises! Our representative man has invented writing and hats. He has not yet invented shirts, however, and I suspect that what he’s writing is My Little Pony slash fiction. It takes time to progress.

Then, Aristotle. Man has forgotten how to shave. He has, at least, evolved to the point of having half a shirt — clearly, a transitional form. Of course, the most important thing is that he has invented Thinking, or at least, staring vacantly while scratching his neck. He could be thinking about My Little Pony, but at least he’s not being obvious about it anymore.

Darkness follows. The next two and a half thousand years are unimportant and nothing of consequence happens until, at last, with a coruscation of light beams, Ayn Rand invents planets and stars while scribbling Libertarian rape fantasies with Objectivist rationalizations.

In the next phase (not shown), humans worship the god-like Rand to the point of paying $14,000 for cheesy paintings that portray her as the pinnacle of evolution, and thus begins the Fall of Man.

I have to weep at this Art. It tells a grand tragic story.

This is the sea slug Glaucus atlanticus, called the Blue Dragon.

Isn’t it lovely? It gnaws on Portuguese Man O’ Wars (men o’ wars?), eating the nematocysts and concentrating the toxins in those many pointy dark blue frills. Look at them and admire their beauty, but do not touch.

A dead pig was caged 300m beneath the sea, with a camera trained on it, as a subject in forensic research. It has a…visitor.

Let me tell you the hard part about writing about epigenetics: most of your audience has no idea what you’re talking about, but is pretty sure that they can use it, whatever it is, to justify every bit of folk wisdom/nonsensical assumption that they have. So while you’re explaining how it’s a very real and important biological process that is essential for development and learning and behavior, half your readers are using the biology to confirm their biases about evolution and inheritance, and the other half already know all the basic stuff and want to get to the Evisceration of the Wrong, which is always the fun part anyway.

So I’ve split this post in two: there’s a section on the basics of what epigenetics is, and there’s a section on what epigenetics is not, and why. Read whatever part floats your boat.

[Read more…]

It’s beautiful: the devil’s fingers, AKA the octopus fungus. Even just the name is like a barbed hook calculated to draw me in.

It has other interesting features, besides the awesome appearance.

While unappealing to us humans,

Stop right there. Am I not human? Did I not coo in delight when I first saw this lovely organism? Do I not want to see my grassy yard replaced with thousands of erupting fungal eggs?

But do continue.

what you’re seeing is actually a rather ingenious method of reproduction. The tentacles are laced with a foul smelling tissue, specially formulated to attract flies and other insects. When bugs come-a-knockin’, they get to feed on the slimy substance, but not before their feet are coated with fungus’ spores.

See? What’s unappealing about all that?