A nose balloon too far

This great dead beast greets me every morning — it’s a cast of a Triceratops skull mounted across the atrium from my lab. It’s impressively large.


One thing has always bugged me about it, though. See that tiny hole directly under the horns? That’s the eye socket. It has a beady-eyed look, like mere eyeballs were an afterthought to long pointy sharp horns.

But then you go forward from there, and what you see is this massive cavity where the nostrils would go. It’s freakin’ huge. You could fit both hands in there, and it goes all the way through the skull. I’m a moderately gracile human being with a skeleton that’s delicate and fragile compared to a dinosaur’s, and I don’t have a giant gap in my facial bones that you could punch through without smashing up a few bones.


What’s up with that, I’ve always wondered. There must have been some impressive fleshy tissue in there, associated with olfaction? Or thermoregulation? Or what? Someone really needs to get right on that time machine idea.

Darren Naish has a far out, speculative, wild hypothesis: those giant meat holes contained colorful inflatable nose balloons for sexual display, because dinosaurs were weird.

I don’t know. It kind of detracts from the majestic dignity of the animal to imagine it puffing out what would look like a gaudy snot bubble to appeal to a mate. What self-respecting beast would do that?


Next thing you know, these paleo guys will be dressing dinosaurs up in flamboyant plumage. No dignity left at all.

First clinical trial of human gene editing

Get ready, world, scientists are going to use CRISPR/Cas9 on human patients for the first time, extracting a population of cells, modifying their genomes, amplifying them in tissue culture, and then injecting the modified cells back into the human host. It’s being done in China, where the ethical constraints are a bit more loose, which isn’t always good…but in this case, it sounds like a good, safe (as safe as experimental therapies can be) approach.

They intend to use CRISPR/Cas9 to knock out the PD-1 gene in immune system cells. PD-1 is a cell surface molecule on T-cells that inhibits the cells, and acts as a constraint on immune system activity. The “PD” is short for “Programmed Death”, and what it does is compel the cells to commit suicide when stimulated — so if immune system cells get a bit overzealous and go on a rampage attacking healthy cells, they can be switched off. The immune system has multiple checkpoints to prevent it from going rogue, and this procedure will remove one of them. By knocking out the PD-1 gene, the scientists are creating particularly unrestrained cells that they hope will do a more effective job killing cancer cells, because cancer cells are known to use the signaling mechanisms that tell the immune system to die.

Are there drawbacks and risks? There are always drawbacks and risks. This technique is a variation on an existing pharmaceutical approach, which uses drugs that inhibit PD-1 in cancer patients, so we know a bit about its effects — it’s just that taking out the whole gene with CRISPR/Cas9 is a dramatically thorough way of demolishing the molecule. But we do have some drugs, like Nivolumab and Pembrolizumab, that target PD-1 already and are in clinical trials. We’ve also experimentally knocked out the gene in mice.

So, we have an idea of what could go wrong, and in the immortal words of Dr House, it’s lupus. Or lupus-like effects. By jacking up the immune system and removing one restraint on its activity, you can get complex system-wide problems, which Dr House will tell you are pretty hard to treat, but at least they’re not as severe as terminal cancer. They are also editing a terminal cell type — it’s not going to proliferate — so eventually, we hope after they’ve killed cancer cells, the injected cells will die of natural causes and the effect will fade away.

This is not a treatment that affects the germ cell line, so these patients, if they survive, will not be passing on an edited gene to their offspring. It’s also got to be a rather expensive therapy that has to be customized for each new patient, so it’s not going to be routine. It is a first step into the exciting world of genetically modifying humans, though.

Not “gill slits” again!


Troy Britain got blocked from the Institute for Creation Research facebook page because he criticized this comment:

Shouldn’t students be skeptical when they’re told that evolutionists can simply look at folds in embryos and see gill slits? The truth is that these are only folds of tissue in the pharynx region of vertebrates during the pharyngula stage of development. For mammals, birds, and reptiles, they never develop into a structure that is in any way like fish gills.

Britain has a good rebuttal in his article about “gill slits”, but I just have to point out something.

I’m an “evolutionist”. I don’t think any creationist would argue with that.

I teach students. Again, that’s indisputable — that’s my day job.

Furthermore, I teach relevant subjects: developmental biology and evolution.

But despite the fact that I ought to be example #1 for this terrible crime the creationist is condemning, I have never taught that all vertebrates have “gill slits”. I don’t know anyone who has. I took comparative anatomy and physiology in the 1970s, ages ago, and my instructors were all very explicit about the function, development, and evolution of pharyngeal structures. I would have been dinged badly if I’d made the mistake of suggesting that the pharynx was primitively a respiratory structure, rather than a feeding specialization.

It is quite correct that in most tetrapods, pharynx structures don’t form gills — gills are specialized derivatives of pharyngeal pouches, just as are hyoid arches and jaws. No one knowledgeable claims that humans develop fish-like gills. “Gill slits” is a colloquialism, not a technical term.

I am amused by the dismissal that they are “only folds of tissue”. Yeah, right. Your brain was only a fold of tissue in the pharyngula, too. Your major organs were mere diverticula. Your eyes were just outpocketings of the neural tube. Mere, just, only. Let’s all dismiss fundamental developmental structures as silly piles of cells, since, as we all know, mere cells do nothing, unless we’re trying to argue that they’re so darned complex that only a god could have created them.

Quaint relics of the pre-Internet era

Who else remembers the days of the BBS? Back in the 1980s I used to hang out on various dial-up bulletin boards, before the internet. They weren’t truly interactive — some used only a single phone line, a few fancy ones could handle a couple of simultaneous connections, but generally you’d log in, browse a couple of messages other people had left, maybe leave one yourself, and log out again, all at 300 baud. When the fancy 1200 baud modems came out (I bought one that was military surplus), my old Apple II struggled to keep up with the furious data rate, and I actually wrote my very own telecommunications program — in 6502 Assembler, of course, using the wonderful ORCA macro assembler package — and took the daring step of cutting a lead on my mother board to enable interrupts, and building the program around a custom interrupt handler just so it would stop dropping characters. I was a true nerd.

It all came rushing back with this article in the Atlantic, The Lost Civilization of Dial-Up Bulletin Board Systems. I abandoned them in the 1990s when the Internet became ubiquitously available, although still often through dial-up lines from home. Apparently some tiny number of them still hang on. There are actually 20 dial-up BBSes still running, somewhere?

But every mass extinction has its holdouts. Even today, a small community of people still run and call BBSes. Many seek the digital intimacy they lost years ago; 373 BBSes still operate, according to the Telnet BBS Guide, mostly in the United States. Many are set up to be accessible via internet-connected tools like Telnet, a text-based remote-login protocol originally designed for mainframes.

Did any direct-access, telephone-dial-up BBSes survive the internet’s proverbial asteroid? Sure enough, there are about 20 known dial-up BBSes in North America. And of those, only a handful have been running non-stop since the mid-1990s. These are the true dinosaurs walking among us. Who dares to run such antique systems, and why? Have any of them been left running by accident like the BBS in my dream? I had to find out.

Yes, why? I want to know. It turns out that many of them are just kept up for nostalgia’s sake, but others are…are you surprised to learn that they’re maintained by delusional right-wing paranoids?

Ten years ago, when I dipped back into BBSes, I still got a sense that many sysops ran them to provide a libertarian alternative to the internet. Among them, the unoppressed who wanted religious freedom, the unsurveilled who wanted freedom from surveillance, and those prepping for the day when BBSes would provide shelter after the internet came crashing down.

It was never an alternative to the Internet. It couldn’t be. You’d have to argue that the Post Office was just a slow version of blogging if you go down that path.

Behe is still comfortably ensconced in a niche of ignorance

Back in the 1990s, when Behe first came out with his idea of irreducible complexity, I recall that there was some consternation in our little community of anti-creationist activists. Behe had done something novel: instead of denying all of the accumulated evidence, he instead turned the focus on the gaps in our knowledge. It’s something of a cunning plan, if you think about it; the scientific literature is full of papers where scientists say that now we understand Step X, but we still need to figure out Steps Y and Z, so let’s work (and get funded) for Y. In a sense, it’s brilliant, because instead of relying on creationist ignorance to advance his argument, he would use honest scientific ignorance instead.

So, have we worked out every single step in the evolution of the blood clotting pathway? No? Then all the gaps are filled in with God Design. Flagellum? Nope. Must have been design then. Resistance to anti-malarials by plasmodium? Clearly, if you haven’t isolated every genotype in the progression of the resistance, there is room for an invisible magic man done did it.

His other clever shuffle was to admit that there are natural processes at work, so every evolutionary change is the consequence of both the understood mechanisms and what he claims are necessary miraculous events, but that you can’t always tell which steps are caused by mutation/selection, and which are Designed. Which means that the scientists have to do all the work of documenting every step, while Behe sits back, does nothing, and gives credit to his unnamed Designer for all the parts that aren’t done. As Matt Herron points out:

Dr. Behe admits (in The Edge of Evolution) that there is “…great evidence that random mutation paired with natural selection can modify life in important ways,” so his view is that life’s diversity and complexity are best explained by a combination of natural and supernatural processes. In fact, I think that’s a fair summary of intelligent design in general. So to falsify intelligent design for a particular example, it’s not enough to show that natural processes are mainly responsible for its origin. No, you’d have to show that supernatural causes played no role at all, no matter how minor.

That’s the funny business that has kept him going for a quarter century now. He doesn’t have to do the work of showing that any of his hypothetical supernatural mechanisms actually operate anywhere, he does not have to test for Design, and in fact he has zero positive evidence for any of the processes that he claims must have been ticking away for millions of years. Meanwhile, real scientists have been measuring and demonstrating the phenomena described by modern evolutionary theory — drift, selection, recombination, etc. — and identifying specific instances of these mechanisms in action. Behe shrugs them off. He’s built a rationalization that allows for the existence of natural processes while demanding that all of the gaps be filled in with his Designer…who seems to be a reflection of his Catholic faith.

It’s infuriatingly dishonest, but he’s found a thriving niche. All the scientists think he’s a kook, while all the creationists who are so gullible that they believe in a great flood and 6000 year old earth look upon him as some kind of super-scientific genius.

Now I have an excuse!

We haven’t raked the leaves that fall in our yard for years — it’s part laziness and partly because we have a corner lot in a windy part of the world, so they don’t hang around much. If we do anything, it’s to mulch them with our lawn mower and leave them in place.

And now I have vindication! we’re helping to protect the environment (warning: autoplay video at that link). I guess I’ll just keep on keeping on.

Now I just need a justification to stop mowing the lawn.


This is too true. Academics face a very confusing career transition.


Of course, it also varies. The post-doc chart is a fairly accurate illustration of my life before getting a position, but the assistant prof chart will depend on what kind of position you land — mine would be much, much heavier on various duties associated with teaching.

The screwy thing is that there is no teaching at all as a post-doc, so the thing we spend most of our time doing now is the one thing we got no training in.

We have a BigBro442 problem

You knew it was coming. The technologies are developing to introduce us to virtual reality games, and right away, there are men showing up to ruin it all.

I wasn’t as experienced a player as BigBro442. Everywhere I ran, he appeared beside me, ready to grope as soon as the zombie wave was over. I’d had enough. With a final parting obscenity, I yanked the headset off my face and stood back in the sunny, familiar room of my brother-in-law’s home.

What had just happened? I hadn’t lasted 3 minutes in multiplayer without getting virtually groped.

There are no penalties for that sort of behavior in the game. There is no one looking on to see that someone is having a miserable experience in what should be fun entertainment. BigBro442 — even his chosen name is a tip-off that he’s a creep — is more experienced in that particular game, which means he’s been playing it regularly, and hasn’t experienced anything to drive him off, unlike the woman who would write that piece.

We just shrug and accept that there will be assholes in games. It’s people like BigBro442 who convinced me to abandon multiplayer games — that, and the developers didn’t give a damn. Every game is targeted right at the young male jerk audience.

Contrast that, though, with what happened when two women went on a date, and the creepy real-life version of BigBro442 started harassing them.

Here’s what happened when the man started asking me and my date about our private lives: First of all, not one, not two, but three employees — two men and a woman — rolled up on this dude, like a very refined food-service gang. Then, everybody behind the bar looked up, watching the scene, and you could almost hear them all thinking Just make one move, fool, I swear to fucking God. I realize now that the staff had been watching us for some time, trying to measure our level of discomfort at an intervention versus their obligation to their customers to maintain a chill, relaxed atmosphere. I’m going to guess that some of these staff members were LGBTQ folks, but all of them were the strongest allies I’ve ever met in my life.

The manager then spoke clearly: “Sir, you need to leave. You’ve made our patrons uncomfortable, and we do not tolerate this kind of behavior in THE BRANDY LIBRARY.” That’s a hilarious statement, but it’s also a very beautiful one — especially when you’re a scared twenty-something on your first big date with a person of the same gender, and you just want to have a nice night.

Wow. That’s how you do it.

It sounds like The Brandy Library is a good place to visit in New York…hey, wait a minute. I looked at the photos of the interior, and the address, and I think I have been there, years ago. But it had a different name. I think?

Well, gosh, I guess I’m going to have to visit New York again and check it out.

I’m not so keen on checking out yet another multi-player video game with little boys running rampant.

Continental circulatory system

It’s pretty. But you know, we could use this map of the American river basins to figure out where to do a lot of fracking and run oil pipelines to maximize the size of the area we poison in the center of the continent. Somewhere up on top of the large purplish area looks good.

Maybe we could put a big nuclear waste repository in the middle of the orange area, while we’re at it.

I sure hope no evil geniuses get any ideas from this.