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You don’t even want to know

But until I come up with something suitable for public dissemination, here, have a fun thing.



Enjoy! Leave comments there!

The Emperor’s Decrees

The Emperor sneezed. Even the torrential downpour hadn’t settled the spring pollen. Curse those catilies! Everyone planted them for the vibrant pink blooms, but he was violently allergic. There should be a law.

The Emperor looked down at the paper he held. No, ninety decrees was enough, even if he’d forgotten the catily flowers. One couldn’t expect one’s subjects to bear too much.

The Emperor stepped out from the doorway where he’d huddled against the rain. Scattered hailstones crunched underfoot. He could feel each one through the worn soles of his boots. Nobody was in the square, but the Emperor knew they would come.

“Decree the First: There shall be no talking goldfish in municipal fountains.” This worried him. A goldfish had spoken to him yesterday while he was washing his face.

It said, “Blurble blurb,” and he couldn’t figure out what that meant, but he knew it was important. The Emperor didn’t want the goldfish repeating its message to his enemies. The simple solution was to ban all talking goldfish in public places. He’d never seen a goldfish swimming on the cobblestones, so he only needed to ban them from the fountains.

A little girl in a grubby dress stopped before him as he read the fourth decree, the one about encouragement of fireflies. They should be offered food and drink in exchange for their flickering lights. He didn’t know what exactly they ate or drank, but that was why one had advisors, to attend to such details.

The little girl threw something at him. He was momentarily distracted by the way her pigtails swirled as she pulled her arm back, then released, but he still managed to dodge the whatever-it-was, and it splatted on the cobblestones behind him.

The square filled with people, flushed couples arm in arm, a few with stern-faced chaperones. The musicians must be taking a break, giving everyone a bit of fresh air before they returned to the whirl of the dance. The Emperor raised his voice, pleased to have such a large audience for his decrees. “Fifteen. The dreadnaughts of the Empire shall be kept free of limpets at all times.” He was a bit fuzzy on what a limpet was, perhaps a large goldfish, but the Emperor was quite certain that they did not mix well with his navy’s ships.

He sneezed again. His throat was getting rough with reading all these decrees, but the Emperor knew that he could make it through all ninety. He was the divinely-anointed Emperor, and he could do whatever was needful. He read on.

“Forty-three.” He was interrupted by a pair of his city guards before he could start to read the body of the forty-third decree.

“We’re sorry, Your Emperorship, but there’s been a threat on your life. You need to come with us, and we’ll protect you. The Emperor recognized the guard who spoke. The man was a loyal subject, often protecting him at night. The second guard grinned foolishly at his companion. The Emperor saw, but chose to ignore the man’s disrespect.

“I must finish announcing my decrees to my loyal subjects,” he replied. “You may wait here until I’m finished.”

“I don’t think so, old man,” the second guard said. “We’ve got orders to bring you in. You’re disturbing the law-abiding citizens, the ones who ain’t crazy.”

The Emperor folded up his ninety decrees and tucked them into his breast pocket, his hands shaking. He would read the next batch tomorrow evening. Eventually his subjects would have heard them all, and the best empire in the world would become even better. He followed the guards, secure in the knowledge that they would protect him for the evening, keep him warm and out of the rain, maybe even feed him. They didn’t bother to take his arms; he’d never given them any trouble.

He felt for the tiny gold coin sewn into the hem of his tattered jacket. It comforted him to feel it there. It reminded him of his mother when she was happy. Before she died screaming, bathed in her own blood and that of his father, as he watched through the fringe that concealed his hiding place.

His father’s face was on the coin, though the Emperor never dared take it out of its concealment to look at his features, so like what he saw reflected in the fountain. Before he got old, at least, and without so many goldfish.

Sometimes, late at night, the Emperor wished his mother’s face had been stamped on the coin instead.

This is another twitter-inspired short piece. I collected prompts, and spent under an hour plotting and writing. No revision, no editing; what you get is what you get, but they’re a great antidote to writer angst.

Tonight’s prompts:

the Universe: 90 decrees (geometry typo); catilies (fascinating captcha word)
Nick: dreadnaught; harassment
@quasigeo: hailstorm; contra dance
@notmoro: fireflies
@notanyani: allergies; pink
@jaymgates: mismanaged schedules; talking goldfish; pigtails
@ravyn the Incredible Mr. Limpet

Solving all my scientific problems

From my email:

Media For Rapid Publications
Invited Reviews

Do you feel scientifically isolated? Do you find yourself sitting on the side-line while others take the field by the nose and lead it? Are you unable to publish a model that summarizes your data and ideas because reviewers label it as being too speculative and unsupported? Can’t get those experiments published in any regular journal? Do you find that nobody is citing your papers? Haven’t published in your field for some time, but want to show that you are still a player? Well, no need to worry! There is a special category of publication for you, ‘the invited review’.

Our consortium invites reviews for following journals:
Journal of X
Journal of Y
Journal of Z
… and a whole bunch more!

Public Service Announcement

Or two of them, actually. [Edit: three, really.]

PSA1: Dumping Swedish fish down your throat is never a good idea. If you are driving at the time, it’s a truly horrid idea.

PSA2: Crashing your car into a parked van may in fact dislodge the stuck Swedish fish, but it is not a generally-acceptable alternative to the Heimlich maneuver even if you are the kind of dumbass PSA1 is aimed at.

I was out for a stroll, walking on the right side of the road in
the grass. Harrisonburg is a proper American city, and has neither sidewalks nor safe places to cross busy roads, so I was just going around the block for some air after driving all afternoon.

An SUV comes whipping around the corner, jumps the curb, hits a parked radio station van in said radio station’s parking lot.

Mid-20s male driver gets out of the car, says he was choking, still in some distress.

I don’t have my phone, so I try to get him to give me his, but he can’t find it.
Some other guy comes wandering up, calls 911 for me, then leaves again (!).
So I stay with Mister Dumps Swedish Fish Down His Gullet, torn between trying
to get him to sit down in case he’s more hurt than he thinks, or
leaving him up to finish expelling Swedish fish.

EMS shows up, letting me dump the decision on people who know what they’re
doing. Fire truck shows up, cleans up spilled car juices, makes sure the car won’t explode.

Popping a smashed hood open with a fire ax looks kind of fun.

As the only witness (road was empty when this happened), I waited around for the
cop, who took a while to show up. According to the EMS people, it had been
incredibly busy for a Monday. I think the cop was pleased with my report. I’m fairly organized anyway, and when out walking in a strange city with no sidewalks, I’m very aware of where all the other cars and people are.

I am entirely fine, drinking beer and eating a sandwich back in my hotel room now.
I still don’t have my talk for tomorrow finished… but I’m drinking beer anyway.

It wasn’t until after, while I was loitering around waiting for the cop, that I realized how close I’d come to being flattened myself. But then, if I’d left three minutes earlier I would have missed the whole thing. There’s just no way of knowing, and no sense in worrying about things I have no control over.

But I ate dessert first tonight, just in case.

PSA3: Discussion on twitter prompts me to remind you all that basic first aid and CPR/AED training is available across the US from your local Red Cross chapter. If Mr Fish had needed help with the obstruction, I could have done so. Why? Because I have CPR certification, and that class covers choking, along with other useful things.

Having basic certs does not obligate you to provide care if you don’t feel able, but it does give you the tools to deal with life-threatening situations. Having certs also offers you legal protection as long as you act within the bounds of your training. If I’d bruised Mr. Fish while dislodging the obstruction, he couldn’t sue me. (Not that I ever touched him, as he was conscious and breathing.)

It’s a good thing to do, and you never know when you might need it. Out for a stroll in a strange city, perhaps.

The good bits

My favorites for the day:

John Scalzi’s new fantasy project: “The entire fantasy series is entitled The Shadow War of the Night Dragons, of which the first book is called The Dead City.” Go read the prologue. Really.

Bagicalupi and Watts start a shared world anthology, guaranteed to drive you to despair and drinking.

Charlie Stross becomes cheezburger.

Google announces its annual new technological breakthrough.

Good science, and weird

I love XKCD, and never more than today.

(Real slime mold, real name, real research. Of course.)

And then there’s Transformer Owl, a Friday treat.
(Sorry, I’m having embedding issues right now. But go watch it.)

From there, the science gets weird:

Yeti research!

Government officials in Siberia are planning to set up a special research institute dedicated to the study of yetis following a number of recent mysterious sightings of the folkloric creature.

Hominology experts???

Capitalism destroyed life on Mars.

I got nothing…


Today let’s take a break from the Great Old Ones and talk about the very important topic of zombie preparedness. I know there’s the temptation to slack off at the holidays: eat too much, spend too much, pay insufficient attention to potential zombie attacks, but resist the urge.

(via Danabren)

For today’s science tidbit, the Parasites of the Day blog is doing the Twelve Parasites of Christmas. Enjoy!

If you’ve made it this far, you might like some nice reassuring sheep.

Science and more science

It occurs to me that I forgot to tell you all that I have a new post up at Science in My Fiction, and that SiMF has moved to its own domain. This month: deep sea vents and giant pogonophoran worms with no mouth and no gut. (And isn’t pogonophoran the most wonderful word?)

I’ll be taking January off at SiMF, but have posts for early February and early March on the calendar. Anything you’d like to know more about in the general area of biology/ecology of science fiction/worldbuilding?

I am really, really enjoying Harry Potter and the Methods of Rationality. I only read fanfic when someone points me at something that sounds particularly interesting–not because of any disdain for the form, but because my to-read list is already substantially greater than my available time.

Disappointing news on the arsenic-using bacteria. I’m not a molecular biologist and not at all competent to evaluate the methods used, but scientists who are(technical) say that the study is seriously flawed, and probably doesn’t show any such thing. Expect a longer post here when I have a bit more time.

Just in time for the Solstice season, Cthulhu ringtones from the HPLHS, even seasonally appropriate ones like “Carol of the Old Ones” and “The World in Terror and Madness Lies”. I need a better phone!

In a poisonous soup

Edit: A disappointing follow-up.

I spent some time this morning tracking science and nonsense in advance of NASA’s press conference on astrobiology. Now that I’ve had a chance to watch the press conference and read the Science paper, here’s a rundown on what the scientists actually found.

First off, here’s the citation and abstract for the Science paper.

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
Felisa Wolfe-Simon, Jodi Switzer Blum, Thomas R. Kulp, Gwyneth W. Gordon, Shelley E. Hoeft, Jennifer Pett-Ridge, John F. Stolz, Samuel M. Webb, Peter K. Weber, Paul C. W. Davies, Ariel D. Anbar, Ronald S. Oremland
www.sciencexpress.org / 2 December 2010 / 10.1126/science.1197258

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

So first of all, this bacterium is not at all alien, nor is it evidence for a long and distinct evolutionary heritage. It’s a member of a well-known group of bacteria, the Halomonadaceae, and thus firmly placed in the standard evolutionary scheme.

Bacteria that use arsenic for respiration in the same way that we use oxygen are also not a new discovery. Scientists have known about arsenic-metabolizing bacteria for a decade or two. Drs. Felisa Wolfe-Simon and Ronald Oremland were involved in identifying arsenic-metabolizing bacteria in Mono Lake in 2008.

Mono Lake

So why is everyone so excited?

When I was teaching introductory biology, I told my students about CHNOPS. The most abundant elements in living organisms are: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur – CHNOPS. There are other trace elements necessary for life, like the iron in your hemoglobin, but those are the big six and everything needs them.

Or so I thought until today. These bacteria can thrive without any phosphorus at all, apparently using arsenic instead in all their biomolecules, including genetic information and metabolism.

Dr. Wolfe-Simon and her colleagues had the idea that it might be possible to substitute arsenic for phosphorus. The two elements are nearby in the periodic table, and behave similarly in reactions and compounds. (That’s what makes arsenic so poisonous to most organisms: it interferes with phosphorus use.) So she went looking, and where better than Mono Lake?

The experiment she used was both very simple and elegant. She collected bacteria from Mono Lake. It has lots of arsenic and bacteria that were already known to metabolize it. Put the bacteria in flasks with everything they need, but no phosphorus and plenty of arsenic, and see what grows. Take those, and put them in new flasks, again with arsenic and no phosphorus. Repeat for a bunch of bacterial generations, until the phosphorus that was in the bacteria when they were collected is incredibly dilute. (Not gone, unfortunately. There’s no easy way to get rid of what was originally there.)

At the end of this, Dr. Wolfe-Simon had bacteria that were living on arsenic without phosphorus, and they were doing fine. She could raise them without phosphorus, without arsenic, but not without both. And when she fractionated the arsenic bacteria — separated them into components, DNA here, proteins over there, and so on — each fraction contained tagged arsenate in the same proportion that she would have expected to find phosphate. That isn’t proof that the arsenic had substituted exactly for the phosphorus, but it is very suggestive.

Swapping out minor elements isn’t new. Octopuses have blue blood because they use copper-based hemocyanin instead of iron-based hemoglobin to transport oxygen. But these bacteria apparently have swapped out one of the major building blocks of life, something that changes our perception of the conditions under which life could be found.

This kind of switch might be beneficial in environments with low phosphorus availability, but using arsenic is inefficient. Arsenic forms weaker chemical bonds, so it takes more energy for repair and maintenance. The arsenic bacteria grew more slowly than those with phosphorus available. They also looked different: bigger, and with more open space (bigger vacuoles) inside.

Bacteria grown with phosphorus
Bacteria grown with phosphorus

Bacteria grown with arsenicBacteria grown with arsenic

Yesterday, we could have ruled out terrestrial-style life on planets without phosphorus without even looking. Today we have to check them out.

And also, I need a new intro biology book.