Good for you, University of Oregon

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There are some things you simply aren’t aware of when you’re immersed in an environment — and that’s the case when I was living in Oregon. I don’t recall Dunn Hall, which was one of the campus dorms, but then I didn’t live in the dorms, and was only vaguely aware of the undergraduate students. I never heard any discussion of Frederick Dunn, the guy it was named for, and who was a classics professor in the 1920s. I especially never heard that he was an Exalted Cyclops of the KKK.

But now people are talking about it, and the university is stripping his name from the roster of buildings, prompted by an act of vicious racism.

Student body president Quinn Haaga urged the trustees to act in the wake of the death of 19-year-old Larnell Bruce in Gresham. The black teenager was purposefully run over by a white supremacist, according to police reports.

“The state of Oregon has a very ugly racist history that was deeply ingrained in our policies and laws,” Haaga told the trustees. “Unfortunately, as this horrible tragedy illustrates, these sentiments are still very alive and well in many parts of the state.”

I know what argument some will use against this: there go the SJWs again, erasing history to signal their virtue, and maybe even comparing it to the erasure from official photos of Communists who lost favor with Stalin. But how can you erase history if you never knew it in the first place? This is an act that acknowledges horrible attitudes that were simply taken for granted. It made me conscious of a founding bigotry that I would otherwise have not known. Eugene is a lovely place to live, but you’re really swimming in a sea of whiteness while you are there (I live there for 8 years), and it’s easy to oblivious to Oregon’s history of sundown towns and anti-black laws.

But here’s one person who defended Dunn.

UO alumnus David Igl made an unsuccessful plea to retain Dunn’s name, saying the professor was involved with civic organizations — such as the YMCA and the Methodist Episcopal Church — that would be antithetical to the KKK’s views. He said Dunn was “a victim of some swindlers called the KKK.”

Hucksters from the South, Igl said, recruited KKK members in Eugene in the 1920s, using fear and bigotry as motivators to part townspeople from their money, but the townspeople soon were disillusioned.

Dunn didn’t repudiate his membership, as far as historians can tell, but Igl contends that few Klansmen did out of fear of the so-called invisible empire of the organization.

Oh, right. No racism in Oregon, just high-minded civic responsibility. The white founders of Oregon weren’t racist, no sir, it was all imported by sneaky bad people from Alabama and Georgia and Mississippi who crept across our border like reverse carpetbaggers, tainting the virtuous liberal egalitarianism of the pioneers. Except…

When Oregon was granted statehood in 1859, it was the only state in the Union admitted with a constitution that forbade black people from living, working, or owning property there. It was illegal for black people even to move to the state until 1926. Oregon’s founding is part of the forgotten history of racism in the American west.

The South is a convenient scapegoat for racism, and yes, it has a history of racism too…but I’ve lived in Northern states, Washington and Oregon and Pennsylvania and now, Minnesota, and the racism is thick and strong here, too. We just don’t see it in action when we’re only hanging out with our white friends, and when we avoid confronting it. I only learned yesterday that there’s a house flying a confederate flag here in Morris, Minnesota — we’re all pretty good at closing our eyes.

I also learned that the University of Oregon is now planning to rename Deady Hall. I didn’t know Dunn, but I certainly knew Deady Hall — it’s the oldest building on campus, very prettily antique, but now I find out that Matthew Deady, one of the founders of the UO (although I knew he was actually opposed to the university system, and didn’t want a university, although he was happy to grab control when it was founded) was pro-slavery.

See? We don’t talk about these uncomfortable facts, until someone waves them in our face, and then we’re all embarrassed and decide that maybe we shouldn’t be naming prominent racists as heroes of our institution.

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.

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.

[Read more…]

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.