What is Aleppo?

Gary Johnson didn’t have a chance of winning the presidency, anyway.

I’d say goodbye, except there’s another candidate who has continuously demonstrated appalling ignorance who is currently running in second place, so I don’t really think this will make any difference at all. Sadly.

All about the pants? Really?

This is Jana Shortal. She’s a Minnesota TV news reporter.

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She recently reported on a news story that’s really shaking up the state. Decades ago, before my time, Jacob Wetterling, a young boy, was abducted at gun point, and ever since, his family has been searching for him. This was huge news locally; long-time residents are surprisingly familiar with the case, which caused emotional ripples all across the region when it happened. And then, just recently, the kidnapper confessed, and in wrenching detail, described how he molested and murdered a crying little boy. It has brought up a lot of horrified responses, which are entirely understandable.

Shortal reported on the story.

Then a gossip columnist for the Star Tribune, CJ, reported on the reporting, and complained about Shortal’s clothes. Her jeans were inappropriate.

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Shortal has responded very effectively — you can tell who is the better writer — but still…you’ve got a murdered child, and CJ made it into a fashion statement, as a story that was all about the pants? Remember, it isn’t about how you feel or what you say, what matters is whether the clothing you wear is sufficiently conservative when you say it.

And the thing is, there was absolutely nothing offensive or disrespectful about how Shortal was dressed. That’s what she wears to work. It’s not radical, it’s not trying to shock viewers, it was a pair of jeans.

There has been a warp in the space-time continuum

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I remember asking my parents to let me stay up late on a school night to watch Star Trek, when it first came out (Thursday at 10pm? What What rat-buggering monkey troll at CBS planned that bit of scheduling?). Now I am told that that was 50 years ago. Exactly 50 years ago today.

That’s impossible. I’d remember 50 years passing by. I’d feel different than that 9 year old boy right now, and I’m sure all of you would agree that I’m just a little kid. With a beard, sure, but still the same.

I consider this to be concrete evidence of a totally mysterious physical phenomenon, and I demand immediate research into this strange time warp, before I take a step to the left and become further unstuck in time, or fall further back into the future.

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.

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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.

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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.

What about the men?

I get asked that question all the time, since I’m at a liberal arts college, and face it, the women are taking over. So here’s an article wondering about those poor suffering men.

“I actually feel like women are taking over the world,” says Ishwar Chhikara, a 36-year-old investment officer at an international development bank, citing statistics showing more women now have college degrees in the US than men. He says this laughing, but with no audible irony.

“I feel bad for men, especially those who don’t go to school, or study. The whole system is changing drastically with the coming of the information age. It’s not about strength anymore, it’s about the brains.”

While muscles at the center of an economy made the physically stronger sex have more power, Chhikara isn’t so convinced with the switch-up.

“It is a positive thing from a woman’s perspective, from a man’s perspective I don’t know.”

The statistics are true, and I consider them kind of inevitable. Here’s my explanation: as we generally improve opportunities, the people who have historically had less than satisfactory outcomes are more eager to improve their situation, and are more likely to take advantage of those opportunities. The groups that have historically had an advantage are slower to recognize that they need to work to keep up, and in fact may resent that they have to jump through a hoop to earn what they used to be simply given. So the current situation is actually a consequence of past inequities and men’s sense of entitlement.

There’s another factor, too: the social stigma of feminization. Look at what happens to occupations associated with “women’s work”, like nursing and teaching. They get paid less, and men actively avoid taking up the occupation. I worry that some of that is happening to universities, as well — we see, for instance, that liberal arts colleges are particularly attractive to women, so why would a man go there? Too many of them are looking at the performance of those manly athletic teams in order to determine where to go.

You find it hard to believe that a winning football season could influence people’s decisions to make an academic commitment? Look up the Flutie Effect, and be horrified.

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.