27 February, 2009

The Laws of Mad Science

The Laws of Mad Science
As set forth by the International Mad Science Judiciary Committee, April 17th, 2008 at the Lair of Raw Power in the Deep Southern Pacific (not the other Southern Pacific Lair of Raw Power).
1) Mad Scientists shall build their machines/equipment/experimental apparatus much larger and more badass* than strictly necessary for no apparent reasons other than that they have the ability and capacity to do so.

2) For each time a Mad Scientist asks the question “why?” s/he is hereby also required to ask “why not?"

3) Mad Scientists are encouraged to integrate disparate pieces of machinery into the same chassis and/or wiring schemas whenever doing so adds aesthetic value but not additional functionality [1].

4) Practicality must not be a concern of Mad Scientists at any time.

5) While Mad Scientists are expected to be creative and generate many Mad Ideas at a rapid rate, we note here that we discourage the recording of those ideas on non-Self-Destructable paper as they may be used as evidence in usurpation by assistants or in a civilian court [2].

6) Due to past security failures, Mad Scientists are forbidden from using either word or numeric puns and/or jokes as passwords, machine commands, and/or entry keys [3]. Cultural references are also strongly discouraged [4].

7) Mad Scientists should develop their own or be fluent in another’s cryptography schemas to encrypt inter-Mad Scientist communications and/or sensitive data. Alchemic symbology is now effectively banned.

8) Mad Scientists are hereby reminded to avoid putting chemical or biological samples into the same storage areas as their own food**.

9) Mad Scientists are banned from conducting human research [5]. We emphatically recommend not practicing self-experimentation (the Mad Scientists' Assistants Congress has asked that we implore you to not use them for experimentation). We condemn experiments on civilian subjects [6]. However, if you determine that a human organic system is vital to your research, please contact this body and we will provide you with zombies ad libitum.

10) Mad Scientists may not steal raw materials from cargo transports, be they naval, aerial, or land-based. This is too obvious and endangers yourself, your peers, and the continuance of Mad Science. You may, and are encouraged to, "re-purpose" abandoned or found materials.

11) Collaborations between Mad Scientists are encouraged and are required to follow the rules and procedures laid out in the Collaboration Articles of 1989 [7].

*In memorial to Sir Puj Dramke (1903-2005).
** In memory of Dr. Bartholomew Töppledigöts (1963-1999).
[1] For additional explanation, please refer to the 2005 case of "Oscilloscope inside Flow Cytometer Chassis".
[2] Dr. Ernstrüm Leipäkirja, 1888. "Bayern gegen die Furchtexperimenten Herr Doktor Leipäkirja." The state of Bavaria convicted Dr. Leipäkirja of diabolical intent and ran him out of town with pitchforks and torches. Dr. Leipäkirja was later reported (unsubstantiated) to be living and working in Puxico, Missouri, The United States of America.
[3] In 2007, 10 years of work by Drs. Pram Tiddly and Evox Evox Exox to develop artificial egg environments for embryonic chickens was destroyed when animal rights activists smashed their equipment after gaining access to their lair by guessing the password "toget2theotherside".
[4] In 2003, black hat hackers invaded the pre-sentient computer network of Hermes Plodd and reconfigured it to sell Viagra just as it was learning its first contextual words. He had used "HAL2000" as a password.
[5] The 1800s as a century led to this ban. The actions of Drs. Jekyll and Frankenstein so imperiled the continued existence of Mad Science that this ban was deemed necessary and incontrovertible.
[6] In 1974, Leroy Natty was convicted and jailed for mopping a disco dance floor with androgens solubilized in DSMO to test the effects of increased libido on the power of social mores. He was also permanantly evicted from the Mad Scientists' Association for his actions. Lest you judge him too harshly, it should be noted that reconstituted artificial human biological systems were unavailable at this time.
[7] In 1988 the collaborative laboratory space of Drs. Ruthie Blandry, Sandeep Ravapredavhanamuran and Xing Zhang were found abandoned and charred. An investigation revealed that each had been keeping data from each other, which eventually resulted in a catastrophic firefight between Drs. Blandry and Ravapredavhanamuran. Most of their bodies were recovered, while Dr. Zhang remains unaccounted for and is presumed dead.

The Laws of Mad Science are meant to be a living constitution and are reviewed and amended as needed at the annual Mad Scientist Symposium. If you have any additions, deletions, changes, or retractions that you believe need to be considered for this year's upcoming conference, please append them below and they will be taken into consideration (please also leave your identifying Mad Scientist credentials, as anonymous or unverified suggestions will be rejected wholesale).

26 February, 2009

Toaster's Late to This Party, Apparently

Rep. John Conyers (D-MI, 14th district [Detroit]) has introduced legislation into the House of Representatives, H.R. 6845, the "Fair Copyright in Research Works Act", that will apparently effectively prevent the public at large from accessing publicly-funded (e.g., NIH) research. This is bad, and in my mad opinion, also rather stupid. I don't think it is inappropriate to compare this to buying a book and then finding that the pages are all glued together.

This issue has been covered by the Scimese over at ScienceBlogs in great detail already (this is why I am late to the party). For broader commentary, check out Coturnix from Blog Around the Clock here and here, Greg Laden here, and Effect Measure here.

What I do not understand is the why of this legislation. ARRA had a clear purpose: beginning to fix the economy. However, this act just seems recidivist and arbitrary. Scientists are not publishing dangerous methodologies and subliminal evil schemes along with their important research, so unless the sponsors of the bill believe that the American people are too stupid and fragile-minded to read raw research and thus must be protected, I don't know why they are doing this. Or, wait, are we too dangerous to be allowed to communicate with the public? Are they afraid we're going to corrupt their constituents with logic, reason, research, and mad science!? Are we all so diabolical that we need to be contained? Maybe this is just the first volley and soon they'll be installing public relations officers at all MRUs whose job it is to Taser us whenever we attempt to speak to the press...

Well, I do have a sign on the door of our lab with everyones' names and the undertitle "Keeping otherwise dangerous minds off the streets and in the lab." Think about it, if scientists intensely curious about the physical world weren't in the lab doing science, wouldn't we probably be doing it at home in much more dangerous conditions instead?

I was under the impression that the big science publishers were not profitable or big enough to have the clout to write this bill, but maybe there have been arcane corporate mergers or something that have made them more powerful than we know (suddenly PLoS seems like Link up against Ganondorf and Zant at the same time). As far as I know the corporate entities of Science, Nature, et al are not publicly held and as such aren't profit driven like the businesses in the RIAA.

My Point:
I have contacted Rep. Conyer's office to ask them why this legislation has been deemed necessary. They said they'd call me with the information once they've gathered it. I'll be posting this conversation as it progresses.

Tesla Coils + The First Law of Mad Science

From Biopunk:
And just how small can one get a Tesla coil these days? I will be looking up more for sure, oh great uberlord of the skies...
While appealing to my megalomania is a good way to get my attention, misunderstanding the entire point of having a zeppelin is not a good way to do so. I have a zeppelin, I mean, a motherfucking zeppelin!, and I can guaranfuckingtee you than I am going to have some gianticmothefucking Tesla coils on board.

So you're really going to ask how small can one get a Tesla coil? For real?

Do you not see the title of this blog!?

Why would one even want a small Tesla coil?

This is barely a Tesla coil.

I mean, really? Even when I have explicitly noted below that Tesla is my penultimate scientific role model because he was batshit eccentric (OK, so I'm not really angry about this because I don't expect everything to get read)?

Now this is a motherfucking Tesla coil!

In short, make no mistakes about it: tiny Tesla coils are pointless, and tiny Tesla coils are stupid mad science, even if they are good electrical engineering. Good mad science always makes its machines much bigger and more badass than they strictly need to be, just because it can (this is also the First Law of Mad Science, so learn it well! I will post on the other laws of mad science at some point in the future).

Now, though, since I have just now learned that one can tune a Tesla coil to specific resonant frequencies (how I didn't know this before escapes me), I am going to go incorporate that into my zeppelin's coils.

Meanwhile, please vote on the poll to your left to appease my ego and enjoy the video below (which I post even through The Legend of Zelda: Twilight Princess is currently frustrating me because I finally beat the giganticbastardtentaclefish in an underwater fight and now I find I am stuck playing as a wolf again! Ocarina of Time, though...they'll probably never top that).

25 February, 2009

Mad Science: Zeppelin

I picked up the local newspaper this morning and, sonofamothercrap!, someone managed to snap a picture of my zeppelin! I was out piloting it around town, low, just above the trees, the freezing winter air humming gently through my 3 jet engines (they're quiet because they funnel air into dense little triangles), in "light-bending" stealth mode no less, when someone on the ground below got this picture (I don't know exactly how they got this perspective, I wasn't close to any of the high-rise buildings in town, but maybe someone in one of them has a long-range camera). I mean, it's reassuring that this photo is so blurry; my stealth features are obviously working to some degree, but obviously I'll need to work on improving them. It could be that the power draw from shooting my plasma cannon (yes, it does have a laser sighting bead, and no my floaty isn't filled with combustible hydrogen, it's got MegaHelium instead [it's fun to go to concerts and vent the floaty at the stage]) weakened my cloaking devices and allowed some light to bounce off of my hull. Maybe I'll have to be more careful and more discriminating in choosing which asshats' shoes I melt to the pavement while they're wearing them (if you intend to wage war against me [ahem, Hermitage!], I recommend you start wearing wooden shoes, like clogs, although I cannot guarantee that they won't combust). For reference, that meshy grill looking thing at the front is about 7m high.

Still, though, I've got a sweet ride, huh?

Still, not as big as this:
This is the Graf Zeppelin in flight over Danzig.

One day I will build one that big, and it'll even have an improved secondary drive train (even better than the current TurboPolka auxiliary system) and a self-contained laboratory(!), and on that day that I launch it and hover menancingly against a stormy sky...on that day...you will need new underwear, or something...and stuff...Yeah! It's gonna be awesome! Of course, I'm going to need fancier goggles and a couple of Tesla coils mounted on the rudder, just for extra (Victorian? Steampunk?) street cred.

Sometimes I think that perhaps I was born into the wrong century...but only until I remember the Internet.

24 February, 2009

Not-So-Mad Science: How EHEC Finds and Spoons Your Gut Epithelium

Figure A: This is a picture of mouse cecal epithelium infected with EHEC. EHEC is FITC green, actin is red (that's smooth muscle to the right of the picture, I didn't have the concentration of phalloidin high enough in this slide to also stain epithelial actin), and nuclei are blue with DAPI. It's at 40X, I think. I usually take prettier pictures than this.


NOTE: This post discusses some animal research. If this offends you, go somewhere else.

Enterohemorrhagic Escherichia coli (EHEC) is an enteric human pathogen that has been the cause of many food-borne disease outbreaks over the past 3 decades. One of the most famous outbreaks was borne by Jack-In-the-Box fast food restaurants in contaminated beef and the most recent outbreak was a spinach scare of 2007 when cow manure was used as fertilizer and then improperly washed. The primary manifestation of an EHEC infection is bloody diarrhea (hemorrhagic colitis), although intestinal cramping is apparently also common. In most cases in most adults, EHEC infection is just very unpleasant and complications are rare. But when complications do arise, they are nasty and life-threatening. The primary complications are sepsis and hemolytic uremic syndrome (HUS). HUS is characterized by thrombocytopenia (low platelet count), hemolytic anemia (exploding blood cells), and uremia (acute renal failure). Thrombosis can be widespread and lead to microangiopathy in the gut, kidneys, and CNS.

Doesn’t EHEC sound friendly? This is why you should always cook your beef very very well, because EHEC doesn’t cause pathology in cattle like it does in humans (we don’t know why yet, either), and also because EHEC can establish a productive infection with an inoculating dose as low as 25 CFUs (CFUs = microbiology term, approximately equivalent to 1 bacterial cell).

Epidemiologically, patients hospitalized with HUS usually have stool (poop!) samples positive for EHEC, specifically strains of EHEC that carry the genes for Shiga toxin. In vitro tests with Vero cells (a kidney cell line from monkeys, I think but am not sure that they’re from African green monkeys, also known as vervets, that are disappointingly not actually green) and human glomerular epithelial cells have shown that Shiga toxin is directly cytotoxic to these cells. There is not yet a good animal model for the pathophysiology of HUS. When mice are injected with Shiga toxin, they develop some kidney damage, but none of the wider complications. When rabbits are injected with Shiga toxin, they quickly develop neurological symptoms, but the other symptoms remain unreliable. And did I mention that the LD50 for Stxs are generally in the micrograms/kg body weight kind of range? Fun, huh?

Most EHEC strains make Shiga toxins (Stxs), which are AB5 toxins N-glycosidases that cleave specific bases on the rRNA, thereby shutting down protein synthesis and killing target cells. Not all EHEC makes Stx equally, and different strains of EHEC carry different types of Stx. From a diagnostic standpoint, this gets confusing.

Thankfully, EHEC isn’t invasive like Shigella, Yersinia, or Salmonella species. That is, it doesn’t disrupt the epithelial barrier in the gut and directly invade the underlying tissue. This isn’t to say that this won’t happen later on in infection when gut epithelial hemorrhage becomes more widespread. It’s more to say that EHEC doesn’t have the machinery to mount a direct invasion. However, EHEC does snuggle up to the gastrointestinal epithelium (GIE) quite nicely (not as cute as one might imagine). It even convinces the GIE to build it a nice little actin pedestal. Basically, EHEC cozies up to the GIE and assembles a Type III secretion system and then shoots a bunch of proteins into the GIE cells (see? I told you is isn’t cute), most prominently Tir (translocated intimin receptor). These proteins are then naturally inserted into the outer membrane of the GIE cells, and EHEC has the ligands for these proteins, mostly intimin, already displayed. So EHEC locks on and secretes still more proteins into the poor GIE cell it is humping and these proteins rearrange the host cell’s actin cytoskeleton to form up a pedestal. We don’t know exactly why EHEC forms these pedestals, and they’re really hard to find with fluorescent microscopy (I’ve been trying with infected mouse cecal epithelium), but it thought that the pedestals protect the EHEC from innate immune cells, give it a base from which to multiply and form tightly-adherent micro-colonies, and/or to prevent EHEC being swept out by peristalsis.

But this then brings up the question: how does EHEC find the GIE in the first place? Sure, there’s going to be some random collisions that might result in adherence, but in general this isn’t enough. So, scientists being scientists, some scientists set off in search of an answer to that very question. They’re cited down below.

Bansal et al did some cool in vitro experiments where they examined the chemotaxis, colonization, and gene expression responses of EHEC to epinephrine (EPI), norepinephrine (NOR), and indole. What they found was that EHEC moves towards both EPI and NOR and away from indole. EPI and NOR are produced by human hosts, although the exact in vivo gut levels thereof are currently unknown (any volunteers?). Indole is produced by bacteria. So the authors posit that the GIE is producing EPI and NOR naturally, and that the EHEC are sensing these chemicals and accordingly moving towards them.

These findings were borne out well. This group didn’t just measure the direction EHEC swam in, but they also looked at biofilm formation (EPI and NOR increased, indole decreased) in vitro, looked at in vitro attachment to cultured epithelial cells in the presence of EPI, NOR, and indole (same results), and also at gene expression. Gene expression analysis revealed that Tir and intimin et al were upregulated with EPI and NOR and decreased with indole.

They didn’t look at whether or not EPI, NOR, and/or indole modulated expression of Stx or other non-adherence-associated virulence factors, but this is something I would be interested to see them try. I did twice. An interesting note is that they co-cultured EHEC with HeLa cells (I know, not GIE, but still epithelial) for 3h to test whether or not adherence was modulated. I have done a similar experiment looking for Stx induction under epithelial co-culture conditions, and I found that 0.6% of EHEC were stuck to the epithelial layer within 15 minutes. That might not seem like much, but when you’ve got 10^6 EHEC cells floating around, that’s rather significant (still 6,000 CFUs!). And in 3h I saw that increase to 8.3% of all cells. I’m impressed, aren’t you? However, I never tested my epithelial monolayers (I did this with both HeLa and Caco-2) for EPI or NOR production, nor did I monitor indole levels in any of the cultures. Still, it’s cool that this group was able to begin answering the question of how EHEC finds the GIE without eyes.

I’m still not sure whether or not to regard them as competitors. Either way, they’re at Texas A&M, so maybe they’ve already got it bad enough.

Bansal, T., Englert, D., Lee, J., Hegde, M., Wood, T., & Jayaraman, A. (2007). Differential Effects of Epinephrine, Norepinephrine, and Indole on Escherichia coli O157:H7 Chemotaxis, Colonization, and Gene Expression Infection and Immunity, 75 (9), 4597-4607 DOI: 10.1128/IAI.00630-07

NOTE 2: I do not know what's going on with the font. I guess this is the price I pay for writing this post in MS Word instead of Notepad. There is no meaning to the font being different for separate paragraphs.

23 February, 2009

Bulltripe/Audio Monstrosity

I was going to post a pessimistic load of bulltripe about personal shit. I had thought for a couple of moments that ripping open the colostomy bag that has been my personal life lately and splattering it all over the interwebs would help, but I realize now that the solution to this is, in fact, beer. And maybe a zeppelin ride about town...

In other news, I now have a last.fm account as "ToasterSunshine", so you may grok my musical sensibilities if you so wish to.

It seems that my planned evening of beer and video games has been taken over by creating this audio monstrosity. I haven't yet been able to figure out how to get my voice to not sound like I'm gargling a metal trash can, so here are the lyrics:
I study cells
I study rats
Gotta lean into the microscope
So I gotta hunched back
I got wild hair
And unsunned skin
The department chairs
Are all cranky old men
I use graphs a lot
Math a little bit
10 hours in the hood
But I just can't quit

If you got a problem with my data
I've got a problem with you
So you see you're gonna have to prove that your problem's true
Yo, I'll admit that I'm not inherently brilliant
But my data's always statistically significant
'Cuz, yo, motherfucker, I'm a scientst!
If y'all can come up with better lyrics or want to enter into a collaborative science nerd rap, then let me know.

20 February, 2009

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'.


Remember: you have been warned.

19 February, 2009

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.

18 February, 2009


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.

15 February, 2009

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:

11 February, 2009


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.

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).

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.

10 February, 2009


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:

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.)

06 February, 2009


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).

04 February, 2009


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.