Evolution caught in a movie

It’s a standing joke that creationists demand a complete time-lapse recording of evolution before they’re going to believe it. Joke no more: we’ve got one. It’s a movie of bacteria evolving antibiotic resistance. I don’t even need to explain it, because the video explains everything that’s going on.

Different old joke now: But they’re still just bacteria.

Also, you should be horrified by the power of evolution. It took 11 days for the bacterial population to evolve resistance to a lethal, thousand-fold increase in antibiotic concentration.

Engineering porn

While I’m sure many engineers also found the paint-mixing porn I posted earlier soothing and pleasurable, the diversity of human experience also allows for other stimulants. Like this, the world’s largest engine.

wartsila_engine

The height of a four-story building, the Wärtsilä RT-flex96C is a two-stroke turbocharged low-speed diesel engine designed by the Finnish manufacturer Wärtsilä.

It is designed for large container ships that run on heavy fuel oil. Its largest 14-cylinder version is 13.5 metres (44 ft) high, 26.59 m (87 ft) long, weighs over 2,300 tonnes, and produces 80,080 kilowatts (107,390 hp). The engine is the largest reciprocating engine in the world.

Jesus. There are videos of assembly. Can we call this developmental engineering?

Let’s start one up.

And watch long, slow, lingering videos of the engine in operation. Nothing really happens, but the sound… my future industrial rock band, which I’m calling Wärtsilä (it even has the necessary umlauts!), won’t have a drummer, but we’ll just haul around one of these engines on tour to be the percussion section.

Whew. I need to cool down. Maybe I’ll go watch some paint-mixing videos or something.

I did it again

Yesterday, I showed off a few embryos I’d collected from my fish tanks that morning — they were at roughly the 16 cell stage. Then today, I put up a video of the same beast at 24 hours old. It was a bit busy, because this is the age when they are going through all kinds of spontaneous muscle contractions, so I also anesthetized one of its siblings and tossed that on the scope. Stoned fish are so much more cooperative.

Fish gone wild

I played a little more with Periscope in the lab this morning. First, I showed off my microscope, and I figured that that was enough babbling, and then went off to do my usual animal care chores. The fish kind of went wild and spewed out hundreds of eggs today, so I went ahead and put a typical 4 cell embryo on the imaging system. It looked nice! So I was going to wait a bit and let it divide and show an 8 cell embryo (powers of 2, they really do that), but the next division was in the plane of the screen, so I waited just a little longer and grabbed a picture of a 16 cell embryo. They’re just cruising along, as they do, dividing and dividing.

I also found it really hard to do microscopy one handed while aiming the iPad camera with the other, so you may get a little seasick watching the videos. Sorry. I may have to draft Mary to pretend to be a tripod while I do my schtick tomorrow.

Yep, tomorrow. I’ve got this big pile of blastulae today, and people don’t believe me when I say they’ll turn into little baby fishies in less than 24 hours, so I promised to come back and show everyone what these same embryos look like on Friday morning.

Stop it, Apple. Enough.

Sheesh. Apple announced a new model iPhone, the iPhone 7, and once again, they’ve jiggered cables and connectors. I’m a big Mac fan, and have been since the early 1980s, but there are two things I detest about their products.

  • iTunes is a clumsy, ugly abomination. Why a company with a reputation for clean interfaces persists in retaining this kludge is a mystery.

  • Cables. Fuck but I hate Apple’s constant game of musical chairs. I’ve lived through SCSI (various flavors), weird buses, incessant games with power connectors, firewire, thunderbolt, etc., etc., etc. I have a huge collection of oddball cables and adapters at home and in the lab.

And now, with this new phone, they’ve discarded a simple, robust connector: the simple 3.5mm audio port. The one every other phone and music player has by default; I’ve got one on the dashboard of my car, for heck’s sake. The most reliable connector I’ve got. The one I use for the really nice high quality headphones I just bought.

And what do we get instead? No connector. It uses a wireless signal. And worse, it’s not anything standard — it’s a proprietary Apple signal. The only thing that works with it are Apple’s $159 wireless earbuds…or alternatively, you use a dongle that plugs into the thunderbolt port and has a standard microphone jack.

I will not buy it. It’s dumb. And unfortunately, I’m using an iPhone 4 (which is fine, I’m in no rush to update), and if I were to need a new model, I’m not going to get one that saddles me with an additional battery and has a couple of easily lost overpriced tiny earbuds. Android would look more attractive at that point.

I’m just going to have to hope that they see reason with iPhone 8, and revert back to something standard. They have in the past, many times.

Fins made of straw, easily knocked down

In response to Neil Shubin’s recent paper on the subject, and Carl Zimmer’s summary, the creationist Michael Denton criticizes evolutionary explanations for the vertebrate limb. It’s a bizarre argument.

First, here’s the even shorter summary of the Shubin work. Ray-finned fish have, obviously enough, rays in their fins — rigid bony struts that provide structure. These rays are formed dermally. That is, osteoblasts deposit bone on the surface of a connective tissue matrix to build the rods of bone that prop up the fin. It’s called dermal bone because the classic example is the assembly of bony elements within the dermal layer of the skin.

Another way of making bone is endochondral. You start with a framework of cartilage, and cells within the cartilage (which is what “endochondral” means) gradually replace the cartilaginous tissue with bone. Your limb bones, for instance, are endochondral, starting out as fetal rods of cartilage that were replaced by the action of osteoblasts.

What the researchers in the Shubin lab found is that fish fins, which have dermal bone, and tetrapod limbs, which have endochondral bone, use the same cell signaling pathways and cell movements to build the cellular structure of the limb/fin, but differ in the final steps. Fish switch on the dermal bone pathway, while tetrapods use the endochondral pathway. We have a fundamental similarity than simply uses a different end-product, which ties the assembly of fins/limbs more closely together than we had thought.

Not to Denton, though! He wants to make some strangely saltational argument that these two modes of bone formation are somehow incompatible. I’ll show you his final conclusion, so you can decide to bother with the rest.

In short, my assessment is this: There never were any transitional forms making both dermal bone and endochondral bone. Organisms made one or the other.There never were any transitional forms with fin rays and digits. And I predict that no matter how extensively the fossil record is searched, the phenotypic gap between fins and limbs will remain even as the genetic gap continues to diminish.

That’s an incredibly stupid statement. You make both kinds of bone; your skull, for instance, is largely formed of dermal bone, while your limbs are endochondral. Fish have both endochondral bones (for example, in their vertebrae) and dermal bones (skull and fin rays). The ancestral fish-like form had both kinds of bones. We have fossils of transitional forms with both a central endochondral core and fin rays.

finfossils

We’re done. Denton’s claim has already been addressed and refuted. How can he not know this?

You can just stop now. His whole argument is dead in the water. But you could take a look at the thought processes that led to that stupid conclusion, and they’re kind of weird, too.

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An almost automated fish farm (but not for Minecraft)

I was following @upulie on Twitter, when I saw that she was using this app, Periscope, to give a demo of what she does in the lab. Hey, I thought, I could do that, so I tried it, and gave a tour of my cheapass zebrafish facility (you don’t need the app to watch it). This is not my fish facility.

heustisfacility

That’s the big boys’ and girls’ system at the University of Oregon. So be warned: I just have a single small rack with 8 populated tanks. Also, it’s got nonstop water gurgling and bubbling, so it’s hard to hear me over the pleasant, soothing sounds. My students and I built it out of a plastic rack from Lowe’s, a bunch of PVC pipe, some hydroponics widgets, a big pump, and a cow trough. Our tanks are plastic Kritter Keepers bought from Amazon. The whole thing cost less than $500, and it’s grossly over-engineered. We were basically collecting from two tanks at a time all summer long, and it produced 50-100+ eggs every day, routinely. We’d only need a handful for observations and experiments, and the rest got thrown into an incubator (or down the drain), and the survivors were raised to produce another generation that will be ready to pump out eggs for us next summer. Or I could collect eggs every day during the school year, except that I’m expected to teach, not just play with the fishies.

I should mention that this is also a low-maintenance system. I feed the fish twice a day — you know, the usual sprinkling of a few tasty bits of ground-up invertebrates on the surface — and top off the reservoir and check the water quality once a week. It just keeps going, and would grow and grow if I let it. Zebrafish are so easy.

Periscope is also really easy. I’ll probably try it again later this week; I thought I’d give another tour, this time of my nice Leica scope with epifluorescence and DIC and a Jenoptik cooled CCD camera, which is also a little farther away from the gurgling water system, so maybe I’ll be more audible. Later still maybe I’ll set up some embryos/cells on the scope and give a close-up look at how baby fish are made.

Oh, and if anyone else wants to try some small scale zebrafish production, there are lots of sources. I stole many of the ideas from my pal, Don Kane, who has instructions for a similar little system for zebrafish. Or you can read Lawrence and Mason, who give an overview of basic principles. Kim et al. also published a detailed description of their homebuilt system. Or, if you have lots and lots of money, there are companies that build specialized racks and water systems just for zebrafish, and you don’t even have to get your hands wet or sniff PVC solvent or buy a bunch of interesting valves and widgets that will put you on a DEA list somewhere.

I guess I’m going to have to believe it now

Some people say we’re all standing on a giant rocky ball, which is spinning around — a ludicrously silly claim. But now I guess I have to accept it, because someone actually made a video recording showing it, by stabilizing the image to the stars. When you do that, you can actually see the earth moving.

You know what else is silly? The idea that I evolved from a rock. LaughingSquid is going to have to meet the creationist standard of evidence and show me a movie of that happening.

I know, this happened a long long time ago, which makes it more difficult, but I still have a VHS tape player, so I’ll even accept that antique medium.

Hey, I think my mother still has my grandfather’s old 8mm movie projector, so I’m willing to go even that far back. Checkmate, evilutionists.