A meeting of the minds

Brian Kilmeade interviews Donald Trump. You can stop right there, you say. That is just too much stupid to be borne. You would be right to stop reading now. Don’t click to go on to the next page. Do not click that link.

You’ll regret it if you do.

Last chance! Turn back now! You’ll be happier if you just go read some webcomics instead.

No, really. I like The Non-Adventures of Wonderella. Questionable Content is always good. Maki Naro? Trust me. Anything. Well, not Dilbert. Almost anything.

You’re still reading? What the fuck is wrong with you?

OK, as long as you understand the principle of informed consent, you may continue. The safeword is any kind of gurgled, choking scream.

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None of them ever have a racist bone in their body

The stories of the suspects in the Black Lives Matter shooting are trickling out now. You won’t be surprised to learn that they’re all saying they aren’t racist at all.

His dad says of one that he’s a poli-sci major, and “these kinds of social-political things really interest him, and he was just there to observe”. Right. Just there to observe, while hanging out on 4chan, wearing a mask, taunting the protestors, and watching as a friend flaunts a pistol and starts shooting. I suppose it’s possible his crime was just having really shitty friends, but in that case, I’m sure he’ll helpfully testify against those other racists he was running around with.

You know, I’m a guy who is really interested in creationists, a group of people I despise, and I also care about observing them and learning more about what they’re doing. But my strategy is to be open about who I am, clearly state my position, and observe politely without interfering — I’ve gone to creationist events with friends and students, and what I always tell them is to be polite and non-disruptive and learn…and also document. I guess I’ve been doing it wrong. Maybe if I were a poli-sci major, I’d know to disguise myself, yell slurs at the audience, and maybe take a few pot shots at them.

Also, one of my kids was a poli-sci major, and if he were involved in something like this, I wouldn’t be making excuses for him. This was a crime, and a stupid crime at that, and the perpetrators were all fully grown men in their twenties. You do not learn responsible adult behavior on 4chan.

Making popcorn for the coming tardigrade wars

tardigrade

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.

Something else on my plate

Tomorrow, I’m recording a discussion for British Christian radio (how do I get myself into these things?), on the show Unbelievable with Justin Brierley. I’m talking with Perry Marshall, who some of you may remember yapping around these parts a while back, and who has a book out called Evolution 2.0, which I had to read.

Yes.

I read it.

Dear gob.

Just to help you picture this: he’s an electrical engineer and SEO guy with only the most superficial, and often wrong, knowledge of biology, and he has written a book in which he explains how all those biologists have got everything wrong. I was most entertained by the parts where he explains how there is all this amazing stuff in biology that we never tell anybody about, and one of his examples was something I lectured my cell biology class about last week, and a couple of the examples were things I talked about in my freshman biology course this morning.

In other words, his stunning revelations that will revolutionize evolutionary biology were all known mechanisms that are so well established that we teach them in basic college courses, and often simply take for granted. And he gets them wrong. Wrong wrong wrongity wrong.

But he’s frenetically glib about it all, which is apparently a useful attribute if you’re trying to sell car stereo speakers. It’s not at all impressive when you’re pushing pseudoscience.

Flat white

I took a break from the grading and grabbed a quick aerial shot of the results of last night’s snow storm. Morris is still flat, but at least it has a fresh coat of whitewash.

snow day

I won’t inflict more drone videos on you until I’ve mastered that flying thing. Also, what do you call it, video editing. Yeah, that would be good to know.

Now, back to the stacks!