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I may work in an Immunology Lab, but when you spend your days on the paperwork, you don’t learn a terrible amount about the – you know – science. This is why I seek out anything lay-friendly I can get my hands on. Lately, I’ve been collecting notes on some of the most basic elements of immunology; in this case, it’s been all about blood.

In advance of my attempt to explain it to non-scientists, I offer a quickie introduction to the dreaded Prion. Why is it dreaded?

A prion is a misshapen protein that acts like an infectious agent (hence the name, which comes from the words protein and infection).

Prions cause a number of fatal diseases such as mad cow disease in cattle, scrapie in sheep and kuru and Creutzfeldt-Jakob disease (CJD) in humans. There is no cure and potential treatments are highly speculative.

In recent years, however, biologists have discovered several animals that are immune to prion diseases. These include horses, dogs and rabbits. Nobody knows why.

That’s from a recent piece in MIT’s Technology Review.

Basically, proteins fold themselves. Sometimes, they fold themselves poorly, like when I get fancy with paper-airplanes. When this happens, they can become prions, and those things are bad news. A creature infected with such a disease experiences nervous system degeneration.

The University of Ballarat’s Jiapu Zhang thinks he’s on to something:

Zhang has simulated how these proteins change shape as their temperature and pH changes.

His conclusion is that the immune proteins are more stable than the others because of a salt bridge that connects two parts of the immune proteins “like a taught bow string”. This prevents them from misfolding into an infectious form.

So salt could be the answer? All I can say is follow the data. I’d love to learn that someone has duplicated his findings. All kinds of potential problems with our nervous system could be addressed. So, there.

Mark Hurst kicked off the first Gel Health conference with an talk that should be interesting to anyone who’s had a frustrating experience at their doctor’s office. Within the embedded video below, the relevant span of time is between 3:00 and 7:00.

Simply put, it’s about Mark’s awful experience with a few facets of his health provider. They are, in order of gripe:

1. Called to schedule a flu shot, was told that he could not pass a note to his doctor.
2. Waited thirty minutes to see his doctor.
3. His doctor didn’t actually see him; the attending nurse handled flu shots.
4. The attending nurse is curt and impolite; tells him he can’t see the doctor.
5. Can’t even say “Please come to my conference on improving patient experience” because his soul has been crushed.
6. Has to wait an extra ten minutes to check out/pay his co-pay.

The questions that any of us would, right, have are: Do you feel listened to? Do you feel cared for? Was it efficient?

A Contrast

My primary physician is part of the Virginia Mason Medical Center, and though BRI is affiliated with VMMC, that doesn’t mean I wouldn’t call them on their lousy service. But, my experience has routinely been far more pleasant. Contrast the above list with what I have experienced:

1. Am always permitted to pass notes to my doctor. In fact, I can directly email him at any time. He, or any other designated person, always get back to me in a matter of hours (at most).
2. I rarely wait more than 5 minutes for my appointment.
3. Even if a nurse were administering something as routine as a flu shot, I am always permitted to ask to see my – or any – doctor.
4. The attending nurses are very kind and pleasant, and don’t treat me like a file to be stuffed in a cabinet.
5. I would have easily been able to invite my doctor to attend something like this. In fact, I think he’d be likely to attend.
6. I never have to wait after an appointment. You pay your co-pay upon check-in (which is a blisteringly fast funnel at the entrance to the hospital).

Now, true, I’m seeing my doctor in a large campus. Also true is the fact that VMMC has spent the better part of the last decade completely reworking their administrative back-end. But, is there any reason that a smaller, more agile office couldn’t incorporate, say, basic human niceties into the equation?

There’s some data that suggests that instances of malpractice correlate with the user-experience. In this light, improving processes can be seen as a kind of insurance policy. There’s a whiff of plain-spoken wisdom that I read into all this: people are less likely to sue their doctors if they don’t come off as distant, pompous, jerks.

Among my projects for this year is the creation of some templates for employing Tufte design standards. If you don’t know what I’m talking about, click here and I’ll bring you up to speed.

If you’re designing a book that makes use of extensive graphics and/or footnotes, the Tufte approach is an excellent method. Each page’s layout appears like a two-column document, save that the second column is narrower and used only for side notes. Side notes are a complete replacement for footnotes and references. The former always ends up below all the text and the latter typically appears in a list at the end of a chapter or book.

But, with side notes, data is not divorced from where it appears in the text, keeping relevant information together. When done properly, a printed work appears much cleaner and comprehensible, with no flipping back and forth required.

No LaTeX

Skillful designers use the LaTeX environment for this stuff. From what I understand, this is an immensely preferable method for book-creation techs. But, I am increasingly convinced that some kind of document or template system needs to be available for programs like Word and Publisher.

I can hear my fellow Tufte fans saying, no, no, no. It’s all well and good to say don’t use those – that may be a best-case scenario – but the reality is that many of we administrators are stuck with them. Frankly, I want to see more people using the approach. I’m going to skip the lecture. It’s just like PowerPoint.

To that end, I hope to have some kind of Publisher template constructed this year. It’d be something you can open and edit, allowing for cleaner design but without the headache of an obscure method.

I was thrilled to discover the following two PDF documents, found at this site, that serve as a good guide. I’ll report more as I get the time for my project.

• A Tufte Style Book
• A Tufte Style Handout

Over at the New York Times, John Collins Rudolf has written about a forthcoming game that I’ve heard not a peep about until today. It’s called Fate of the World, and it’s one of those games with a message, which means that I’m cautiously crossing my fingers.

From the NYT piece:

The game relies on climate prediction models supplied by Myles Allen, head of the climate dynamics group at the University of Oxford’s atmospheric, oceanic and planetary physics department.

Change is achieved by applying policies, in the form of cards, to a dozen geographical regions, with each turn representing the passage of five years. Players can promote nuclear power and institute cap-and-trade schemes, or pin their hopes on untested technologies like fusion power or carbon capture and storage — so-called “clean coal.”

But the game does not stop there. Players can take an authoritarian route to save the world, by implementing population controls, like China’s one-child policy or banning the eating of meat. Yet these options can backfire, leading to local rebellions.

“You can dictate policy, but the regions might not like it,” Mr. Griffiths, the designer, said.

Far darker options are available for seriously unscrupulous planet savers. These include sending secret agents to overthrow recalcitrant governments and surreptitiously adding contraceptives to the water supplies of nations resistant to birth control. Those with apocalyptic leanings can even release a genetically engineered virus to crash the world population. (Rudolf)

The game developers have real-live-video-game experience, so I’m holding out hope. This is precisely the sort of game that I’m drawn to. Educational, system-focused, and potentially fun.

Hat Tip to Dave Gottlieb.

There’s some pretty wild stuff going on out there. In addition to all the gee-whiz gizmos our industries provide, university science departments regularly surprise me with the stuff they’re doing. Check this out:

This tickles me. I’m always searching for ways to make our complicated sciences more interesting. Using microscopic lifeforms to control a game seems to be a natural fit. Just wanted to share.

You know you’re a writing-nerd when you encounter a notebook and think, “I have to have that.” Well, the Field Notes brand steno pads are a dream. They remind me of the drawing pads that my high-school art teacher had lying around. During this past Christmas season, I encountered a rack of these things at a specialty paper shop.

Sturdy. Durable. Beautiful. The paper-weight is very satisfying to touch. I think I prefer quality pads precisely because I do so much stuff online. When I’m offline I don’t want to muck about with 99 cent Target pads.

Let’s just say that a pad or two will be on the way shortly. Check out this great making of video. Writing-nerds, beware. Your wallet may get lighter.

Go shopping here.

Today, Paul Basken, at The Chronicle of Higher Education, wrote about a potential dark side of favoring research over education.

Universities are aggressively seeking federal dollars to build bigger and fancier laboratory facilities, and are not paying an equal amount of attention to teaching and nurturing the students who would fill them, scientists say in the articles.

And, some faculty members are getting nervous. Plus, when NIH tightens its belt, many universities get concerned about where additional funding will come from.

And universities have been seeing even more dire budget scenarios at the state level, the traditional foundation of their governmental support. Those worries, and the hope among universities that the federal government might take up more of the load from the states, helped encourage the National Research Council, a private federally chartered institution, to form a study panel of 22 university and corporate leaders. The group, due to issue a report this spring, has been drafting arguments for why the federal government should recognize university science as a national asset deserving of more resources.

…

Mr. Mann said he saw a direct correlation between universities’ promoting and paying for those teaching skills, and improving the quality of science research. Among other problems, he said, universities rely heavily on the integrity of their faculty to produce trustworthy science. “As the pressures become higher for people to generate grant income to support their salaries and their enterprise,” he said, “then the pressure for the absence of integrity gets higher.”

The health of universities, and the overall U.S. economy, depends on finding that right balance, he said. “There’s a real risk at the present time to have a system that’s not stable.”

This is certainly worth paying attention to. As a buzzword, Sustainability means more than preventing farmland nutrient run-off. It applies to a whole host of economic and social institutions.

Hat tip to Nicholas Schiller

Mainstream science reporting is continuing its stellar job of reporting the facts absent context or clear baseline science literacy. I wish political reporting was handled the same way. I want to see more anchormen struggling to follow a train of thought instead of confidently making half-baked assertions. We can all pretend we’re political analysts, but it’s a lot harder to fake your way around a lab.

NASA has announced that arsenic-based life exists here on Earth. And no, it’s not alien. But, it expand the possibility of what evolving life may look like. Ed Yong notes “the results have nothing to do with aliens.” Thanks Ed, but we loves us some aliens. so that’s how it’s being sold. Arsenic E.T. is so cute. Why not buy a key-chain?

Fortunately, I know just enough about biology to find the following segment of Ed Yong’s piece understandable and interesting.

In 2008, Ronald Oremland (who was also involved in the latest study) discovered bacteria in Mono Lake that can fuel themselves on arsenic. Like plants, they can photosynthesise, creating their own food using the power of the sun. But where plants use water in this reaction, the bacteria used arsenic. Wolfe-Simon has taken these discoveries a step further, by showing that the bacteria are actually incorporating arsenic into their most important of molecules.

She took sediment from Mono Lake and added it to Petri dishes containing a soup of vitamins and other nutrients, but not a trace of phosphorus. She took samples from these dishes and added them to fresh ones, gradually diluting them to remove any phosphorus that might have stowed away onboard. And all the while, she added more and more arsenic.

Amazingly, bacteria still grew in the dishes. Wolfe-Simon isolated one of these arsenic-lovers – a strain called GFAJ-1. Using an extremely sensitive technique called ICP-MS that measures the concentrations of different elements, she showed that the cells of these bacteria did indeed contain large amounts of arsenic.

By giving the bacteria a mildly radioactive form of arsenic, Wolfe-Simon could also track where the element ended up in the cells. The answer: everywhere. There was arsenic in the bacteria’s proteins and in their fat molecules. It had replaced phosphorus in many important molecules including ATP. It was even in their DNA, a conclusion that Wolfe-Simon backed up with a number of other techniques. All other life uses phosphorus to create the backbone of the famous double helix, but GFAJ-1’s DNA had a spine of arsenic.

It’s an amazing result, but even here, there is room for doubt. As mentioned, Wolfe-Simon still found a smidgen of phosphorus in the bacteria by the end of the experiment. The levels were so low that the bacteria shouldn’t have been able to grow but it’s still not clear how important this phosphorus fraction is. Would the bacteria have genuinely been able to survive if there was no phosphorus at all? (Yong)

Oh, and here’s the official NASA report. Tenacious little buggers, no? And they’re darling.

I love data pictures. This is why I justify Tufte seminars to my employer every other year. It never hurts to brush up on some basics. Among those basics are: a clean look, plain language, and no chartjunk.

I owe a tip of the hat to Boing Boing for this great pointer to an infographic depicting the history of scientific thought (a la tube-map). My first thought was that the data are useful seeds for growing an interest in critical thinking skills.

The summary is priceless:

500 years of modern science, reason & critical thinking via the medium of gross oversimplification, dodgy demarcation, glaring omission and a very tiny font.

Wry pseudo-apologies be damned; the thing is wonderful. Planting seeds is my thing, so I had to share it. Just staring at the work makes me appreciate the painstaking development of thoughts that I all too often take for granted. It’s worth remembering on the next occasion that I shake my fist at the world. I can be impatient, but change takes time. Dammit.

Click here to directly view the graphic.

Over at Kongregate, there’s a game that purports to be both fun and educational. It purports to teach, but whether it does that well or not is directly related to its ability to engage.

CellCraft

Build a cell, fight off viruses, survive harsh worlds, and save the Platypus species!

This game was made possible by a grant from the Digital Media & Learning Competition. The goal was to make a truly educational game that was also genuinely fun to play. We hope students, teachers, and gamers will all enjoy the game, and encourage you to visit www.cellcraftgame.com, which will soon have an open forum and eventually downloadable teacher materials.

Based on what little I’ve played so far, it’s much better than the bulk of teaching games out there. That is to say, it’s actually fun – and that’s rare.