Positional information and morphogens

Here we go again — I said I’d try to make a youtube video about developmental biology every week, and I’m keeping that promise. I’m thinking, though, that my last couple of efforts were too big and indigestible, weighing in at 40 minutes each, so I’m going to try instead to present brief introductions to basic biology, and see if those are more interesting to people. I aimed for 10 minutes, but hit 12 instead — sorry, I’m a college professor, wind me up and let me go and I won’t shut up.

Let me know if this format is easier to stomach, and suggestions are welcome.

I could take ’em

I watched that terrible Giant Robot Duel. They were slow, clumsy, and stupid, with nothing but ginned-up drama to add some fake excitement to cumbersome machines poking at each other in slow motion. It was like old television wrestling slowed down to a tenth of the usual speed.

At least I realized something. An old flabby guy in glasses, like me, could easily defeat these monsters. All I’d need is a pair of cable cutters to go in and hack random wires and tubes while they plod around, and victory! I’ll say this for the old FAF wrestling nonsense, I know that Rowdy Roddy Piper or Hulk Hogan or any random luchador would flatten me in a heartbeat and with a laugh. These robots were contrived and pathetic.

Also, we already have manned fighting robots. They just aren’t poorly designed to appear anthropoid and aren’t equipped with feeble weapons like paintball guns or chainsaws. Here’s one:

We’ve been working on battle bot technology for about a century now. These things aren’t pathetically awkward and inefficient and useless.

I also don’t think I could take an M1A2 with my aged nimbleness and some wire cutters.

The Bog that Ate Brainerd

Just wait until it gains a primitive sentience and ambulatory appendages. A giant bog has come adrift and is wandering about demolishing docks in a Minnesota lake. It’s so big it has trees growing on it.

We could also wait for The Blob solution: winter will be here soon and will lock it down in a cage of ice. Except that might be the final incentive it needs to break free of its aquatic limitations and rampage across the prairie. We’ll keep you alerted, but in case Pharyngula suddenly goes silent, it may be because I’m imbedded in a slimy matrix of muck and cattail roots and algae.

Racism enshrined in higher ed

Is this what nurses are being taught?

It’s also revealing how white people aren’t even mentioned. We are the standard by which all are measured; our responses are assumed and we just have to mention the differences, like that blacks are inured to pain and Jews complain a lot and Indians are stoic.

I’m not too surprised to see this kind of garbage in a nursing textbook. It’s no criticism of most nurses, but there’s a heck of a lot of bad woo in nursing programs — my university’s bogus Center for Spirituality and Healing is affiliated with the nursing school, to their eternal shame.

I’d feel schadenfreude, except that it’s such a damn sad waste

Alternative medicines: they claim to cure all kinds of ailments, or at best they promise that they’re harmless supplements. Now here comes the data that says some herbal remedies are correlated with increased cancer risk.

According to a study published Wednesday in Science Translational Medicine, traditional components of herbal remedies used throughout Asia are widely implicated in liver cancers there. In Taiwan, for instance, 78 percent of 98 liver tumors sampled displayed a pattern of mutations consistent with exposure to herbs containing aristolochic acids (AAs). These are carcinogenic components found in a variety of centuries-old herbal remedies said to treat everything from snakebites to gout, asthma, and pain.

Because of their toxicity, some (but not all) of the herbs and plants known to contain AAs have been banned in Taiwan and other places. These flora tend to come from the genera Aristolochia (e.g., birthwort, pipevine) and Asarum (wild gingers). The Food and Drug Administration has also issued several warnings and advisories over AA-containing remedies.

Also relevant: patients who replace tested medicines with alternative crap have a 5x higher death rate within 5 years.

There’s a reason there are tested guidelines in place for careful, controlled studies of medicines, and why side-effects and long-term consequences are scrutinized thoroughly. What’s the point of a treatment for gout that works, hypothetically, if it increases your risk of liver cancer?

There are also reasons for ethical guidelines. Take, for example, this experimental vaccine for herpes that was designed by William Halford and backed by Peter Thiel. They bypassed IRB review; they ignored FDA guidelines; they carried out the tests on an island in the Caribbean, St Kitts, to bypass US oversight requirements. They injected 20 patients who really were suffering with serious, chronic herpes infections with a weakened virus, and got mixed results — for some it changed how subsequent expressed themselves, for others, it made the symptoms worse. The researchers failed to demonstrate either safety or efficacy.

And then, to make it even worse, Halford died, leaving the patients and the study in the hands of…who? No one. By abandoning responsible oversight, he’d left the legitimate biomedical authorities free of any obligation.

Maybe Peter Thiel will step forward and take responsibility for this botched and poorly designed experiment.

I can laugh at that idea, at least. But not at the desperate people who take bizarre alternative medicines or leap at terrible forlorn hope therapies.

Stats make me so tired

Just so you know, Jason Thibeault (The Lousy Canuck) is going to do the cunning work of transferring all of my files from the dying Scienceblogs site to the thriving Freethoughtblogs site. At some point in the near future there will a sudden surge of old content, so I thought I’d mention a few stats before they get bumped upward. Pharyngula on Freethoughtblogs has 986,224 comments on 11,009 articles; if all goes well, Jason will be hauling in 831,367 comments (that number is low; Seed Media butchered the comments in their last major update) and 14,387 posts to add to that, so we’ll kind of double in size.

Do you realize that the commenters here have written so much more than I have? And here I thought I’d blocked and censored everyone.

Is the way you say goodbye genetic?

We have this thing called The Minnesota Goodbye — if you lived here, you’d know what I’m talking about. You’re at a potluck where you brought your hot dish or jello salad, and you want to go home, but first you have to find the host and compliment them and have a conversation about the weather and comment on their wallpaper and maybe promise to have lunch sometime which means you’ve got to compare each others’ calendars, and there’s a line of people trying to do the same. It’s agony. My wife, descended from Minnesotans, has this trait. It’s a moral obligation. You cannot leave without chit-chatting first.

Meanwhile, I must have some Irish in me, probably from my father’s side of the family, which means I favor The Irish Exit, so I feel a moral obligation to get out of everyone’s way and stop intruding on my host. If I could, I’d like to snap my fingers and instantly make a twinkling vanishment to reappear at home — not because I dislike the party or the people at it, but just because we’ve all got better things to do than linger.

Now I want to know how native Swedes and Norwegians handle this problem.

The continuing saga of the scientific implosion of the Wansink lab

How can anyone be this sloppy?

Originally published in JAMA Pediatrics in 2012, the study found that children were more likely to choose apples over cookies during lunch when the apples had a sticker of Elmo. Both the original and the replacement claimed that the study included 208 students “ranging from 8 to 11 years old” at seven schools in upstate New York.

But, as confirmed to BuzzFeed News by the leader of the study, Cornell University professor Brian Wansink, the data was actually collected while observing kids 3 to 5 years old.

“We made a mistake in the age group we described in the JAMA article. We mistakenly reported children ranging from 8 to 11 years old; however, the children were actually 3 to 5 years old,” Wansink told BuzzFeed News by email.

As the “leader of the study”, you’d expect someone to have some vague idea of the approximate ages of the subject…you’d at least know whether the school you were testing at was a pre-school or an elementary school. This is what you’d expect of a guy who is great at churning out papers and grant proposals, but is a bumbling incompetent at the science. Unfortunately, most of the rewards of science go to those who excel at the first set of skills, while the second has a low priority.