Anti-Chicken PSA

This (Goat) Anti-Chicken is wearing a disguise.

Do not mistake this more colorful specimen for the real thing, as it could very well be the last thing you do.

You see, the (Goat) Anti-Chickens, they, they is watchin'.

Always.

Remember: you have been warned.

In Which Hermitage Interviews Toaster

The Hermitage herself has demanded I answer her interview, or else she threatened to steal my cookies.

Little does she know that stealing Toaster's cookies will lead to an immediate mobilization of the Toaster War-Zeppelin and a declaration of war. This will involve me following her around in my zeppelin blasting polka (something really annoying like Atomic Harmonik) and the Numa Numa song until she returns all cookies in their original plus interest. If this strategy does not work, I will of course be forced to call in the FTA (Finnish Troll Army).

I did not answer her questions in order.

Favorite organ (any species is acceptable)?

The appendix. This is something I had actually never thought about before, but upon reflection it occurs to me that the appendix is my own little reservoir of all ~10^10 of my very best and closest little friends: my commensal microbiota!

What outfit would you wear if you won the Nobel prize tomorrow (pictures required!)?

See the Punk Music post below. Add a black top hat and that’s it. Maybe a lab coat, too.

Who is your greatest Academic Role Model?

Nicolai Tesla. He was the penultimate tinkerer and mad scientist. And he was batshit eccentric. In many ways, this is exactly what I aspire to.

Zombies vs Vampires vs Werewolves vs Cylons, who would win and why?

This depends on how you quantify the win. I submit 2 scenarios: 1) zombies vs. vampires vs. werewolves vs. cylons fighting each other or 2) zombies vs. vampires vs. werewolves vs. cylons competing to eat/kill/damage the greatest numbers of humans.

Scenario 1:

This is also dependent on who has which technology. If the zombies, vampires, or werewolves have the technology for an EMP, then the cylons are screwed. Since vampires typically have huge lifetimes and structured social groups, let’s assume that they have the capability to develop EMPs, therefore effectively taking the cylons out of the picture in the long term. Then if we turn to fighting prowess, the zombies would fall next because they don’t have any superhuman strength, special longevity, and, because neither vampires nor werewolves are human, they can’t convert fallen enemies to their own ranks. So it’d wind up being vampires vs. werewolves. If we assume the myths to be true, then vampires have the advantage of having their super-abilities every night of the week while werewolves are only in lycanthrope form once a month. However, werewolves also have the distinct and great advantage of being able to be active during the day when the vampires must return to soil from their original graves. So whether or not werewolves win depends on them being able to survive night-time attacks while in their weaker human forms long enough to find the vampire coven during the daytime and destroy it. And since vampires have been hiding out effectively for a very long time, I am going to assume that they are very good at it and as such would destroy the werewolves before they are found and destroyed. So here the vampires win.

Scenario 2:

Zombies would win. Once again, cylons would be out due to EMPs. Vampires and werewolves have a vested self-interest in preserving a sizeable human population to feed off of so that they may continue to exist as individuals. Zombies don’t give a shit. Zombies will eat whatever they can get their claws on because they are no longer fully autonomous individuals (they are driven entirely by hunger) and do not plan for their long-term viability. Zombies also do not have supernatural restrictions on the times of day or month that they can attack and eat humans, which they can also then convert to being more zombies. End effect is that the zombies win and the vampires and werewolves are helpless to do anything more than try to keep a feeder population of humans safe from the zombies.

It probably says much that I have a more detailed response to this question than to any of those above. It's probably now rather obvious that I think Cylons are lame. Daleks are scarier than those wusses.

If you were a Scientific Superhero, what would be your theme song and why?

This one is difficult because there are so many songs that would fit. I’m torn between J.S. Bach’s Concerto No. 1, First Allegro Movement as played by Lara St. John (because it’s such a bad ass piece of music) and “Blitzkrieg Bop” by The Ramones (because it is). However, “Phat with a PhD” by Kid606 is also a strong contender. This would be easier if I were allowed to have a new theme song each day, or else the same song would get tired quickly.

Kukka*

I am not a morning person.

When I have been left alone without any other obligations (when was that, again?), I tend to sleep from 4am-10or12. But now I have a job, and although my boss has been very understanding of this (letting me work 11am-7pm instead of 9am-5pm), it has come time for me to start waking up earlier and getting in to work much earlier (so I stop missing morning deliveries and whatnot). I have tried a couple of different things to do this, but so far none of them seem to work for more than about 1 week. Normally, I like to wake up, brew tea and make oatmeal, walk the dog while they're steeping, and then read online news while I eat and drink. However, this whole process takes about 1 hour (probably because I usually eat ~1kg of oatmeal at one go). So for a week I tried getting up and skipping breakfast and just going to work. However, I don't generally eat lunch, so this didn't work for very long at all as I found myself falling asleep at my desk. So I tried using my cell phone as an alarm and putting it on the other side of the apartment so I'd have to get out of bed to turn it off. This didn't work either. I have also tried eating dinner earlier (~6pm, as opposed to ~10pm) so that the food won't keep me up. This, too, is not working.

So, reader, what works for you? How do you trick yourself in to getting up in the morning? How do you convince yourself that you're sleepy before 2am?

*That is not a new addition to the English language (see "Blurf" below). It's a Finnish word that means "rooster". This seemed appropriate because roosters=morning in Looney Tunes, which I am convinced are more accurate representations of life than any sitcom I've ever seen.

Music: Punk

Without music there's not much reason to wake up in the morning.

Lately I've been listening to a lot of punk music. I mean, I've pretty much always liked punk music, but lately it's just been in really heavy rotation through my media players (as opposed to hip-hop, electronica, drum and bass, avant-garde, classical, or heavy metal). I don't know why, and I don't think it matters why. It's been stuff like The Dead Kennedys, The Damned, The Sex Pistols, Gogol Bordello (the movie above makes me want to grow a moustache), Bikini Kill, The Violent Femmes, The Clash, etc..

I once played bass in a metal band.

I have played bass in jazz band.

I have played bass/cello in an avant-garde industrial jazz outfit.

And I have played cello in several chamber music ensembles.

But I have yet to play in a punk band, and lately I REALLY WANT TO play punk music! I don't know why, but it's something about how fast and loud and brash the music is that draws me to it. And it's not just because it'd give me a reason to pull my Doc Martens and zipper pants back out. It's been a while since I've participated in any collaborative music, and I guess I miss it. I hate shopping for clothing and buying it because it usually never fits, but every rocker, even punks, need a stage ensemble. This'd be mine:

Mendeley

Mendeley just ate ~2.5h of work.

Mendeley is a free (for now at least) program that aims to do much what Endnote, Zotero, and Papers do, but to do so better. It's main edge seems to be that you can outsource your reference library's metadata, and even the .pdfs themselves, to their cloud and thus carry them around from computer to computer without having to continually update lagging versions of Endnote that run on different machines. This seems like a good idea so I figured I'd try it, especially since Endnote has a very annoying habit of freezing my lab computer.

Mendeley's good ideas:
1) Keep reference metadata and .pdfs in the cloud for maximum portability.

2) Automatically parse .pdf data.

3) Parse and display all references of all .pdfs added.

4) Full text-searching and user-editable tagging.

5) Social sharing of your library, notes, and metadata with other users. This seems like it'd be really useful for grad students in the same lab, post-docs in a new lab, and collaborating prinicple investigators.

Sounds good in theory, right? Yeah! However, even for a beta, Mendeley is rather clunky and awkward.

Mendeley's awkward dance moves:
1) Syncing the reference metadata I added (tags, abstracts, notes, etc.) to the cloud completely erased everything I had added. Sure, the .pdfs are now in the cloud, which is convenient, but ALL my notes about the papers are gone like dust. So is all of the cleaning up after Good Idea #2.

2) I didn't expect this to be perfect, and I was fairly satisfied that it worked perfectly in ~15% of papers and got most of it right in 75% more. But now that I've fixed it, and then lost all of that in syncing it, I'm not eager to go back and have to do all of it again.

3) Usually works. Doesn't seem to recognize most, or any in some cases, of the references in papers where the references are formatted at 50% the font size of the text. Haven't tried adding files or notes to references yet, or clicking through to their abstracts.

4) Works, but sometimes pulls in "accepted day X, month Y, year Z" or pieces of correspondence information as well. And not all papers have keywords set aside for this kind of parsing, which the program shows as a big angry exclamation point.

5) I have yet to try this. I figured I'd give it a spin after syncing by data, but now...well, not right now.

I'll most likely give Mendeley another try sometime soon, especially if the bug of deleting corrected metadata (and yes, I remembered to save) when syncing gets fixed. It looks promising and I hope that it is able to remain free (or at least, free for beta adopters?).

At the moment, I'm just glad that I didn't rashly delete my Endnote library.

UPDATE:
I contacted Mendeley about the problem and we're working on it. Hopefully their fix will work. Also, they apparently Google themselves daily, so beware (they're watching).

UPDATE 2:
Fix worked. Now I have 2 folders, one with raw extracted .pdfs, the other with my annotated .pdfs. However, I'm not sure how I'm going to maintain them both.

Blurf

The English language is occasionally wonderous.

Not because its syntax allows for easy eloquence.

Not because it makes sense.

Not because of all of the contradictory pronunciations and bastardy homonyms.

But because it is user-editable. If you need a word, make one up. If you find a word in another language that makes better sense here than a word we've got already, then add it on in. English is like pudding: normally it's gelatinous and silly, but once you add chocolate or something else interesting to it it becomes delicious.

Anyway, today I announce my newest addition to the English language:

BLARF
1) noun; dry vomiting in which one tastes bile at the back of their throat but manages to contain it.
2) noun; a knobby club or cudgel used expressly for hitting douchebags in the gonads.

You're welcome, English language!

(Sometimes I feel it is only a matter of time before the English language disowns me because I keep using words like "happity", "joyness", "beautigent", "intelliful", etc. whenever I get excited and forget that Webster is always watching.)

Career

Today is one of those days where I am wondering why I am trying to be a scientist at all.

I see my PI struggling to pull down enough funding to keep the lab going. I see other PIs in the same boat, always running themselves ragged and noses worn to bloody stumps by the grindstone. I see jaded graduate students swollen with regret and post-docs seething with frustration. Is this what I want for my future?

Once upon a time I had pinned my dreams for the future on this. Now I look back at the myself of then and facepalm violently.

But still, what's to say that in 15 years with lots of experience and a Ph.D. I won't look back at the myself of now and vomit out my ileum in jaded disgust over my possible present naivete? Even now I kinda sorta feel that I should have gone into computer science because it also offers intellectual thrills but without the 20ft. deep mud bog soccer game of scrambling for grant funding. I thought that I was going into a job that'd be thankfully cubicle-free and secure in spite of my plans to go ahead and get into grad school fairly quickly. Although I don't have a cubile, I do have a bench and a desk, so there's not much difference. And security depends entirely upon funding, which is nowhere near as secure as I once believed. I mean, I can certainly get my intellectual kicks from science and I can definitely be happy afloat in a sea of carbonated data and statistics, but I can't eat ideas (I imagine that great sparkly ideas would taste like cookies and terrible bad ideas would taste like rancid butane). The payoff in an academic career is so far away, and the crap to wade through to get there so deep, that I really have to wonder whether it's even worth it in the first place. Yeah, sure, SCIENCE!, but...years and years and years and years and years and years of science, science, and nothing else. I have been happy to create and conduct science, but will science consistently continue to be a source of happiness for me throughout the rest of my life?

Maybe I'd be less existentially gloomy if I'd remembered that whole lunch thing today...

Partly at least I know why I'm doubting my plans thus far. I've invested my time in other difficult things before with no real substantial happiness payoff. Logically, I know that science is not a cello, but still: the point stands. I know that I could put my head down and ball up my fists and plow through everything in my way (sisu!), but right now I'm wondering what the risks of missing almost everything beautiful and joyous along the way are. I know that life aint' all butterfly turds and puppy chuckles; I know that being successful at anything requires major investment of self, time, and energy. I want to sink my teeth into science and tear it a new hole it never knew it needed so badly, yet sometimes I doubt that I'll ever be anything more than just mediocre.

Maybe it's a screwed up way of looking at things, but I'd rather set out to do something and fail outright than to be mediocre in that goal, because then I wouldn't be learning anything...

I'll probably blather on more about this later. For now I should go seek food and find a program to remind me to eat regularly instead of going without food for 10-12 hours at a time (today only for about 8 hours, but 10-12+ isn't unusual for me).

Cookies

Figure A: This IS a cookie (we'll come to the converse later).

Today I am annoyed. I'm tired of not being taken seriously and having to explain myself to collaborators who don't bother reading my Methodology write-ups (do I seriously need to start diagramming these things in my spreadsheets?) to understand the data I share with them. I am tired of collaborators who keep coming around to our isolated little lab looking for results when it's too early for anything to have grown. I am a technician, and yes, I am powerful, but I am not a Master of Timespace. I cannot force bacteria to grow faster, and nor can I make a predict the outcome of the experiment from the first sampling time point. I have done this experiment now what...5 times? And today, today at the first time point of the newest iteration of this same experiment, you tell me that you're not sure the antibiotic concentration is optimized!? You tell me this after I have poured ~300 media plates? For real? You know, when you perhaps should have probably at some point realized that you should test all new strains with antibiotic resistance for their optimal antibiotic concentration. Just sayin'.

I don't like repeating things like this just because the data aren't what was wanted. I don't like wasting mice (germ-free, no less; although that's pretty much all we have) and time and money. And I'm sick of doing quantitative culture. Sure, I can do it accurately without thinking, but still: it gets kind of old.

But today I got a cookie. One of the animal techs had brought some chocolate chunk cookies to an earlier meeting, and she let me have one of the leftovers. It was one of those store-bought cookies full of delicious chemicals to keep it soft and chewy and non-crumbly (guar gum, I think...). So I am going to distract myself by writing about cookies.

First, in praise of cookies:

Cookies are delicious. Of all the delicious sweet foods out there, I believe that cookies are the best. Even with doughnuts, baklava, pulla, bagels, cake, pie, ice cream, pastries, scones (WTF is up with scones, anyway?), zalaybees, cupcakes, etc. out there, cookies reign supreme. There are few things in life better than a warm, soft cookie. Chewy and just a little bit crumbly. Throw in some chocolate or dried fruit and it is wonderful. That moment when you first bite into a fresh cookie and it has that crumbling crust that you bite through into the sweet softness inside is bliss.

Figure B: Toaster as a young child.

You see, when I was young I was a chubby child. I was the kind of kid who maxed out their library card and got tired of the children's section at 8 and the young adult section at 10. I was pudgy, and looking back I realize that at the time I didn't really realize it. I wasn't chubby because I ate cookies all the time (I was chubby because I was, and am, too clumsy to play outside much and I lived in the South with all the wonderfully terrible-for-your-health food), but they were certainly present , and the memories of them are indeed fond. I am no longer chubby, but that chubby kid is still with me, screaming for cookies (and M&M blizzards)...

Now, to throw down on faux-cookies:

There is an important difference between cookies and crackers. Cookies are sweet and chewy and wonderful. Crackers are hard and stale and are still crackers whether they're sweet (Animal Crackers) or dusted with salt and garlic (Triscuts). So stop calling those puny motherfuckers parading as cookies cookies! If you need a "cookie press" to make it and it's crunchy, it is NOT A COOKIE (and yeah, I'm looking at you, Nilla Wafers)!

Figure C: This is not a cookie, and if you insist on calling it as such even after reading this, I will personally find you and come kick you in the face.

We call graham crackers "graham crackers" because they are crackers. We call animal crackers "animal crackers" because they are goat fucked crackers. The only time that it is appropriate to call a crunchy, stamped, baked crackers a cookie is if it has soft filling (a la Oreos, although this may be recidivist hypocrisy on my part, because I do really enjoy Oreos). Call the scabby little bastards anything else, but not a cookie! Call them crackers, wafers, thins, butt crack peelings, whateverthefuck; I don't care! But not cookies.

You see, dear wider society, you've already squeezed all the goodness out of Saturday morning cartoons. You stopped playing good cartoons as soon as I was old enough to want or be able to buy my own cable. And the few good ones that even played after that are now canceled! So you listen to me here, you dusty, boogery bastard, you are NOT going to take cookies away from me either! I mean, shit, Cookie Monster himself now eats vegetables and fruit! What else are you going to corrupt? Are My Little Ponies going to get fashion accessories and Bratz BFFs? Is Dora the Explorer going to get a makeup kit? You've already turned Oscar the Grouch into a wuss, so stop already. Today's kids are going to grow up to be as bland as belly lint, only they'll be able to string together a text message.

Today it is cookies, tomorrow it is our very souls!

An existential question:
Do you think that the traditional cookies of any given culture are reflective of the values of that culture? Furthermore, do you believe that one's favorite cookie could yield insight into their personality? For reference, the best cookies I've had so far have invariably been oatmeal chocolate chip, even better with chopped walnuts and dried dates or something.

Reflective

I was digging through some of my image folders and I found these old cartoons I drew while Bush was still President (hahahaha! Past Tense, MF!). These were originally published in the school newspaper at my undergraduate alma mater.

Crap.

Well, it seems that neither Blogger nor Flickr are willing to accept a 35Mb .tiff file and I don't have any conversion software on my system.

Pretty much what I was going to say anyway:
Suffice it to say that I will miss Bush for one thing: he was easy, and fun, to caricature. It may actually be better for all of you that the pictures aren't working, because one of them was a caricature of Bush in cheerleader drag and such an image may indeed scar your fragile and hope-addled minds. This is not to imply that you are feeble-minded, but that it's the kind of caricature that one needs mental bleach for. Believe me, I know, I drew the thing. It's one of the few cartoons for which I do not regret not having the original drawing.

Oh, wait...I can provide a link to the cartoon on Flickr (SFW, but still not suitable for children; also, please ignore the shit watercolors also there).

E-I-E-I-Obama Hope

Swollen with hope and national pride, I penned this entirely original little ditty for y'all.


Barack Obama has a plan
E-I-E-I-O
A plan for the whole United States land
E-I-E-I-O
With a Twitter, Tweet there
And a data data there
Here a Twitter
There a tweet
He likes information
Isn't it sweet?
E-I-E-I-O



Clearly I am the next Mozart.

But seriously, thank you America. I discovered politics (like discovering yourself, but dirtier) during the Bush era (double entendre!) and for the most part this led me to thinking that, although we have been a great nation before, we were also incredibly stupid and that there was no hope for us. And that we didn't deserve any. At this same time I lived in suburban Midwestern Sprawl, and each week another field or forest would be bulldozed to make way for another copy copy subdivision and Bradford pear trees (which I still despise, and not just because you can't climb them). I saw this as the paving over of our very intelligence, thrift, and resourcefulness. I saw this as a literal and figurative fattening of America (PSA: if you have dozens of hairy flab jelly rolls, please keep your shirt on when jogging||Unicorn Chaser for Bad Mental Image), we drive everywhere and even destroy the possibility of walking or bicycling by not building sidewalks. We build a library and then don't patronize it. We get the Internet but use it only for porn or paying bills. We succumb to the boy-child idiocy of Hannity, Limbaugh, and O'Reilly. And there in the suburban wastelands (intellectually), we mentally rot. A new car is bought, the neighborhood homeowner's association works itself into a self-righteous lather when someone's grass isn't combed right is 1/4" too long, the basketball hoop rusts. And we moulder into our routines. Entombed in cul-de-sacs with neighbors we think are funny-looking don't know but feel we're better than anyway, we do nothing (zombies, but less entertaining). I still feel this way about suburbia. Maybe it's partly bitterness about the sheer blinding whiteness of the neighborhoods, the assumed snobbery over lawnmowers. Perhaps it's anger that each and every forest and stream (except one, and that's only because the hills are too steep to be profitable) I spent my younger weekends climbing through was bulldozed over, filled in, dammed, or destroyed by more mindlessness.

But...

Today there is a hope. I know that it is unfair of me to expect that President Obama will solve all of our problems. I know that it is unreasonable to think that he'll sign away my student debt or approve my PI's grants. But I still hope. This President seems to value actual data and real information. He is communicative, he is bold. And one of the things that has disgusted me for so long about politics is how everyone is so timid that they do nothing meaningful just so that they may numbly be re-elected the next term. Although he is not magical, he is certainly inspirational. If Barry can do it, then so can I. And I can look at my nieces and nephew and tell them truthfully that they can be anything in the world they want to be. If Barry can do it, so can they. And so can we. This is hope, and it feels good even amid the despair of the economy and war because it is the flickering light at the end of the storm. This is hope, and although it will not fill our bellies it can keep our spirits warm. And it is also the hope that pride and joy will replace the past eight years of petty factionalism and fear and anger. It feels good to have been proven wrong about America. We can be better than suburban mindlessness. We can dare to dream bigger than bank transactions and eye-throbbing spreadsheets. We are Americans, and we like tacos! and we can. So let's really begin the 21st century. After all, it's about time.