Removing the Imagine from Imaginal Discs AKA "The Maggot Post"

A friend on twitter posted a little snippet linking to the following site, in the context of using diverse individual (cell) inputs to create a workable synergistic economy. I read the page and thought: "Imaginal cells...I do not think that word means what you think it means." Granted, the above author was referring to a childrens' book about butterfly metamorphosis. Even in that context, though, the biology is a bit...er....wrong. But what are Imaginal Cells? And do they have anything to do with Imagination? Or a stable economy?
So I set off on google to find out, and found this paper.
Granted, this might be totally wrong. I have an undergraduate degree in biology and I've forgotten most everything. So when the author of this paper goes off on microarrays, I only have a vague fuzzy memory of what he's on about. So feel free to flame me if you want. For those of you who don't want to read the paper, here's the real story of imaginal cells, or more properly, imaginal discs.
-Firstly, imaginal can mean "imagine", but in the context of bugs, it means "adult."
-When baby flies (maggots) come into this world, they have two types of cells. One type becomes their internal organs and muscles. The other type doesn't differentiate quite yet. They're all plain, vanilla generic cells. These are kind of freeloader cells while the fly is still a maggot.
-When the maggot starts to metamorphose into a fly, certain patches of imaginal cells, ie. near the wings and near the eyes start to divide, forming hollow disc-shaped structures. These are called imaginal disks. The ever-popular Pharyngula has a nice article on this with pictures of imaginal discs.
-So how do these tumorous disks of plain cells know how to become fly eyes on flies, or catterpillar wings on a butterfly? How come the eye disks don't turn into wings? How come the leg disks don't turn into antennae? They're the same sort of plain vanilla cell, afterall.
-The paper above decides to find out. They have some poor grad student mutilate a dead maggot for various imaginal discs..the wing one, the atenna one, etc. They smash these up, then, they amplify the RNA transcripts in each one seperately. When you amplify mRNA with reverse transcription*, you wind up with a small strand of DNA called cDNA. That's why it's called "reverse transcription." Eventually, they have a bunch of cDNA transcripts from the wing disc, a bunch of cDNA from the eye disc, etc.
-Remember, that in basic genetics, the double stranded DNA seperates in places like a broken zipper, and RNA polymerase will slap base pairs onto the single strand. These are mRNA transcripts which then get sent off to the ribosomes so that they can get translated into proteins. The genome itself has several mechanisms by which it can block transcription or crank up production, winding up with a pile of mRNA or just a trickle being produced by different cells with the same genes. These are called transcription factors.
-The scientists then labeled all of these cDNA bits with a florescent element.
-These scientists then used a microarray to figure out exactly how much each gene was getting transcribed in each different imaginal disk.
-Microarrays are pretty damn neat in themselves. Think of a little chip that has millions of tiny little dots on it. Each dot is a bunch of pieces of the sequence from a different gene in the genome, which each have one end glued to the chip. You can get whole genomes for some organisms on a microarray.
-When you dump a bunch of pieces of flourescent cDNA on a microarray, they stick to their corresponding dot like iron filings to a magnet, and the more of them that stick, the brighter that spot glows when you stick it under a UV light. So, if your imaginal disk has a transcription factor that is bumping up production of gene A and gene B is getting transcribed normally, you'd expect the dot corresponding with A to glow bright green and B to glow a little.

What they found was that there was little difference in the numbers of transcripts for particular genes, on imaginal disks with the same type, ie. the left and right wing, but that there was a very big difference between the numbers of certain transcripts being produced on the wing disc vs the leg disc or the eye disc. Thus, the major difference between the pretty much identical patch of wing-disc cells and the eye-disc cells was the amount of each gene that was getting transcribed. Production of certain genes was slowed down in the wings and increased on the eyes and vice versa.

So, is a wing cell always destined to be a wing disc cell? Can you take a cell from a wing-disc and stick it on the maggot's face and end up with a fly that has a wing stuck to its face when the maggot pupates?
Well, actually, yeah.
This tells us two interesting things. Firstly, the part of the head outside the disk isn't doing anything to turn the antenna disk into antenna. Secondly, even though disks look pretty much the same on the pre-puation maggot, the cells in these areas must have already differentiated from each-other to the extent that their transcription factors can push them towards different ultimate fates.
So, in short, the imaginal cells of the caterpillar don't have any vibrations or harmonies. They also aren't any more of a prime example of creative synergy than any other cell in embryo development. In fact, if I were to pick a unique flower synergy cell, I'd choose the totipotent plant cell which can dedifferentiate and become a different kind of cell if it needs to. That's how you can grow a plant from half a leaf with a little auxin horomone slathered onto it and stuck unceremoniously in a new pot.

*I decided to spare you guys the picture of the guy sitting in a bathtub filled with maggots as an illustration for this. Come on, folks. It's not disgusting if you're doing it for charity! Wait. Yeah, it is. There are definitely parts of my body that I do not want maggots near, thank you. If you want to see some things that you just can't unsee, Google Image "maggots."

** The paper discussed here is

Expression profiling of Drosophila imaginal discs. Ansgar Klebes, Brian Biehs, Francisco Cifuentes and Thomas B Kornberg .Genome Biology 2002, 3:research0038.1-0038.16doi:10.1186/gb-2002-3-8-research0038

***Yes the fly in the picture has legs growing from its face. It's from a paper where they messed with the expression level of a gene called antp in the imaginal disc for the antenna and ended up growing a leg instead.

Tirade on Healthcare

At least I'm honest.

A few notes on healthcare that were too long for twitter. Twitter, by the way is like putting a message in a bottle and tossing it into the ocean. It's addictive, fun, and good for venting into cyberspace.
Anyway, I have a message for politicians of both persuasions. Don't stuff this up. Seriously. Healthcare in this country is a fracking joke to the point that I think I'd rather die than have my relatives suddenly land in a crazy amt of debt for me being in the ICU. My savings would probably pay for about a day of it. I'm insured, but I'm sure the bastards have some way to get out of paying if the price goes beyond a certain amt*.
As to the bumpkins who think they'd rather die than have socialized medicine, you're going to be the ones that are going to be living on the public dole because I'll bet most of you are uninsured. So just suck it up, ok, and make life easier for everyone else.
Firstly, Republicans: We don't agree on much of anything and this is not an exception. I and most voters, when it comes down to the wire, don't give a flying f*ck about being presented with a smorgasboard of slightly differing expensive insurance policies. This is not a valid argument against Public Insurance. Sure, the rhetoric about wanting the government out of your health sounds nice, and it's fun to repeat at the top of your lungs...but think about it. Could the government really do that much more of a craptacular job of providing good care at low costs than private business has? Last time I went to the emergency room, I waited 4 hours, got led to the x-ray room, and then got forgotten while all the doctors and nurses went out to lunch. I spent 30 seconds with a doctor after waiting for another hour and impatiently pulling aside an orderly and reminding him that I was *there*. I got a $2000 bill in the mail of which I paid $200. I'm glad I had insurance to pay for it, but come. on. $2000 to get service that I wouldn't tip for in a restaurant and 30 seconds with a doctor?
Can you imagine what kind of situation my sprained wrist from riding my bike to work would have put me in if I *hadn't* had a job or insurance? If I get to wait 4 hours in the emergency room in Canada but the state covers me, the Canadians are STILL getting a better deal.
So take your "government never does anything right" scare tactics, and shove them, ok? It's not like people won't have the choice to spend a load of money on private insurance if they feel they want it, the rest of us will just have a safety net.

Democrats: You guys aren't off the hook. I have a few words for you to ponder while you're teeing up on your "all expenses paid by your lobbyist buddies" golf-cations.
There are some things big business does well. For example, you know how today Obama and Clinton and Berry mustered up the cojones between them to extend a few Federal benefits to gay couples working for the state? Yeah. Employees of many of the nation's giant evil multinationals have had those benefits as WELL AS full health benefits for a while now. Companies are pretty progressive when it comes to maintaining a happy , profitable workforce. Where they come up a little short is when profit is inversely proportional to peoples' wellbeing. ie. if an insurance can save a boatload of money be refusing insurance coverage to a person with a history of illness, forcing them to pay out of pocket and forcing them into debt, it will.
I always vote for you guys in the odd hope that you might actually do something to change this country for the better, and I'm always disappointed because YOU ALWAYS FLAKE OUT and play politics instead of working towards doing what you know deep down is the right thing to do...the thing most in line with those ideals that you profess to have.
I'm not going to appeal to you to remember the people who voted for you, because honestly, the people working for the pharmecutical companies and insurance companies and medical associations who are now doing their very best to butter you up probably voted for you, too.
I appeal to you to remember that your actions have the power to directly help a lot of people. I appeal to you to remember why you got into politics--probably because you thought you could actually make a difference for the American People. I offer the thought that while a compromise with industry on universal healthcare might benefit those workers at the various lobbying companies and associations in the short term, it's going to have a toll on ALL OF US in the long term.
Lastly, I'd like to suggest that for this country, doing nothing is going to be better than doing something halfassed and ending up with an even more convoluted version of the spaghetti we have now, which is what's going to happen if you guys BUDGE AT ALL ON THIS ONE.

Your Unicorn Chaser

And also,
http://freeworld.thc.org/root/phun/unmaintain.html
How to write unmaintainable code!

A Disturbing Story about a Psychopath

http://scienceblogs.com/pharyngula/2009/06/a_heartbreaking_absence_of_emp.php

Don't read that unless you have a tough stomach.

I posted the following on it in response, because it really bothered me, and I'm reposting it here because I have an ego and I thought it would be a good blog post rather than just a mere comment.

Oh man. I'm going to have to drink some warm milk and think happy thoughts in order to sleep tonight. Thanks for that. I'd really like to say I can't imagine the suffering that poor animal went through, but I can, and it makes me sick to my stomach.
How can you judge a psychopath? A person with no empathy. It's not like Cheyenne was there when they were handing out minds and was like "yeah, I'll take THAT one". She didn't ask for a lack of empathy or to be totally selfish.
It would be a hell of a lot easier if there was a devil. It would be so much easier if people like Cheyenne had just sold their souls to him and then we could say "oh, that person is an evil bastard and will rot in hell" and move on. I think the hardest thing about atheism for me was accepting that no, that kitten did not go to a better place. Yes, the person that killed it is evil, and there's no divine justice that's going to rain down on them. Plus that, how can they be truly evil if they never chose to be evil? There is no way this situation will ever not exist or be made right.

I catch myself thinking as have a few people on the forum that the goons on 4chan /b/ enact vigilante justice from outside. Then I have to check myself--vigilante justice is never a good thing because it has a tendency to spiral out of control. Plus that, that's what this girl wants. She wants attention. What is this if not wishing for divine retribution, or at least some sort of internet superman?

I think sometimes that religion is an easy and comforting way out of thinking about these problems that present a huge moral dichotomy: people who are evil but don't understand that they are or why. It's unpleasant and confusing to think of because the solution is simply accepting that at this point, there is none and that's a hard thing to do.

Top 10 Most Disgusting Things I've Ever Done on Purpose

#10 The Fish Dissection

I got to dissect a pickled crawdad in 4th grade as a part of a science program offered over the summer called Bugs, Guts and Microscopes. The teacher was a really nice middle school teacher who new my mum, but you don't care about that, you want to hear about the crawdad. The crawdad was very tricky to dissect. Its feathery gills were falling apart in the formaldehyde and leaving greyish-brown fishy chunks all over the baking pan filled with wax that served as a dissection tray. Man, those things were foul. Smelly wax filled with punch-holes with chunks of organic debris clinging to their sides. I wondered how they got them clean, or if they even bothered, and who the lucky shmuck was who had the job of cleaning up after us. Anyway, the worst part of the crawdad was that your hands smelled like a truly ghastly combination of dead fish and formaldehyde for days after.
In college, I graduated from crawdads to normal fish. Not even sure what kind of fish it was, but you could tell that it was "fish day" in the biology labs halfway accross campus from the stench. I think in the nine years between fourth grade and college that animal pickling technologies had improved to be less...err...pungent, but preserved dead fish will never be anything but overpoweringly vile.

KQED has Pissed Me off for the Very Last Time

Urg. KQED did a show on the Chevron vs. Trial Lawyers on Behalf of Theoretical Rainforest Inhabitants in Ecuador. Listen to it if you have a taste for shallow thinking and BS. I apologize on behalf of Northern California for this steaming turd of tree-hugging Berkeley liberal propaganda. I also apologize for central California for prop 8, and also for Sacramento for being incompetent, but that's a different post. If you want to hear Chevron's side of the argument, and they get brownie points for being able to provide actual evidence for their arguments, go here.
Anyway, time for another scathing letter to KQED, this time hopefully giving Krasny a damn good spanking for being such a drooling yes-man to a troupe of goons with an obvious agenda. He probably won't read this masterwork...but you can.

Dear Forum,
I was deeply disappointed in your reporting on "Chevron Protests," May 28, 2009. Although your website states that Chevron itself was unable to provide a representative to argue the company's case, I feel your show has a duty to present both sides of an argument that has two valid points of view. Both of your guests were very anti-Chevron and anti-oil, and both of your guests had an agenda which coloured their analysis of the events surrounding the lawsuit between Chevron and Ecuador. It was not made clear to the listener that Chevron never directly operated the field in question, Texaco operated it for a short period of time in conjunction with Petroecuador, the national oil company of Ecuador. Both of your guests made painted this lawsuit as a David vs. Goliath battle between the poor oppressed natives and the evil multinational corporation, and Mr. Krasny made no effort to refute this or to indicate that this may not be a simple, black and white issue. No mention was made of the fact that Petroecuador has operated the field in question since 1992. No mention was made of the fact that almost all profits from the operation there went to Ecuador.
I have a relative who works as a mid-level manager for a large oil company and has worked in places where the state govenment is both corrupt and impotent. In these countries, companies like Chevron often have to broker deals with the local warlords and landowners (some of whom are opposing each other) in order to drill or mine. These deals often involve building roads, schools, and hospitals as well as giving the local officials large cuts of any profits made. These deals can go south, often when the local warlords reneg on their contracts. My relative has coworkers who have been killed or directly threatened when gangs of thugs lay seige to the office and plant with automatic weapons. To always paint the multinational as evil and oppressive, and the local regimes as being used and manipulated is both factually wrong and a disservice to your listeners. It is entirely possible that these local officials perceive an easier time and a bigger dollar in suing Chevron to clean up Petroecuador's mess than in trying to get their own government to pay for it.
In conclusion, Chevron is not evil or corrupt. Chevron is a corporation that exists, like all corporations do, to make money. It is owned and operated by average people with families and kids to send to college and food to put on the table. It is simply not cost effective or profitable for Chevron to polute the rain forrest. It puts them at risks for multi-billion dollar lawsuits and it inhibits diplomacy for future exploration within the area. The people who stand to gain from this lawsuit are corrupt local officials and trial lawyers. This was not refuted with evidence from your interviewees.
In short, this program was the far left equivalent of hosting a show on the ethics of torture with special guests Dick Cheney and John Yoo, and with everything boiled down to black and white heroes and villains. This is a pretty lowbrow view for KQED to espouse, I think.

Sincerely,

And, oh yeah. I'm not continuing my subscription or giving you clowns any more money. Ever. Thought that might be a bit of a cliche ending for the letter, though.

The Housing Bubble has Popped? You don't say.

I was listening to NPR in the car on the way home (KQED again. didn't have any fresh podcasts for the commute. I wanted them when they started into fundraising, let me tell you.), and they were discussing, yet again, the housing bubble.
What gets me is that everyone is still scratching their head over the fact that it popped! "We could have never predicted this!" and "Isn't hindsight 20/20?" and "I thought it would never end!"
Funny thing is, I know jack shit about economics, finance, banking or real estate, but if you'd asked me a year and a half ago, I'd have told you that the housing bubble was going to burst. I couldn't have told you when, but frankly I was hoping for sooner rather than later, and I couldn't have told you how. But I could have told you that the housing bubble was dangerously overinflated, and dependent on a large fraction of money which simply didn't exist.
Now that I think about it, I can't understand how anyone with any sort of umbilical cord to reality could have *not* seen this coming.
It's like totaling your car in an accident where you hit a cow. They're not camouflaged and it's not like the cow jumped out in front of you. You had to be blind or high or stupid or drunk or all of the above to have a car smash with a cow.
I grew up in one of the cheaper parts of the midwest. My family was upper middle class at the time, and we lived in a small house, which my parents sold. They put the money towards a bigger house. My family had loans, but my mom always found enough cash in the till to make the monthly payments. My father's income was such that he could afford to pay off the house in less than thirty years.
Cut forward twenty years. I've moved to California. I make about what my dad made when I was a kid, and don't tell him this, but I think I have roughly the equivalent "rank" at work that he did. My friends are starting to get married, and with marriage comes the purchase of their fist house--they usually try to find one in a good neighbourhood with a preschool, just in case they find themselves with kids in the comming years. The problem is, with what they are paid, around 60K a year apiece, 120 K with both husband and wife maintaining a fulltime job, they can't afford to make any sort of normal monthly payments on ANY houses in the area. This includes the ones near the train-tracks on the bad side of town. House prices in California in 2007 are greater than 10 times more expensive now than your average Utah house twenty years ago (lest you think this is an invalid comparison, houses all over the west have increased in price by large factors. Of course, we all attribute this to the damn Californians).
But wages are about the same.
So my friends would take out these massive loans which they knew that they could only pay off through selling the house at a price that was significantly greater than the exhorbitant price that they had paid for it. The only thing keeping these people out of massive debt was the faith that their house was worth more than what they paid for it, which was sold for more than the previous person paid for it and so on. These houses hadn't actually had anything valuable added *to* them. In some cases, I reckon the wear and tear of 20 years of family usage probably devalued the houses.
So, the question comes down to--what's going to happen when one person can't pay off this debt they've gotten themselves into? What happens when they can't afford the expanding interest on their "bubble" loans because these loans are given on the premise that they have money that they cannot possibly have with today's wages? What happens when this happens to a bunch of people? What happens when the bank finds out that a lot of money they'd counted on having from these loans simply doesn't exist? What happens when people who are already scrambling to pay their mortgages get laid off?
*Pop*
If you didn't see that one coming, you weren't looking, and if it was your job to *be* looking, then you'd better get to work finding a solution. Hint: the solution is not doing anything and everything in your power to raise house prices again, and it doesn't involve giving loans or credit to people who cannot by any arithmetic trickery afford the loan they want.