Potty Talk

In keeping with the childish theme of rewriting Christmas Carols, I read over on New Scientist that there's a particularly egregious and difficult to stem form of environmental pollution in which we are all engaged.

Using the potty.

According to the article, "Despite making up only 1 per cent of the volume of waste water, urine contributes about 80 per cent of the nitrogen and 45 per cent of all the phosphate. Peeing into the pan immediately dilutes these chemicals with vast quantities of water, making the removal process unnecessarily inefficient."

The article goes on to describe (in a lot of detail) the sewage disposal system and how, unless you're a green European you're pretty much destroying the environment one flush at a time.

The only part I'm unclear on is once you've separated the urine from the "grey and black water" (eww!) and put it into tanks where "microbes" break down the nitrogen and phosphorus, what are the actual by products of this whole effort? According to the diagram on the website, the "sludge" (again eww!) is either brought to a landfill or incenerated. Isn't that contributing more methane (a potent greenhouse gas) to the atmosphere? What they really need are the methane convertase bacteria which I suspect we'll find any day by a hydrothermal vent in the deep ocean.

So just in case you were feeling self righteous about driving your Prius or not even owning a car (like me) remember that you're no different from that Hummer driver, every time to pop a sqat.

Jingle Balls

Julia Ward at TV Squad reports on the latest assault on Christmas by... Charlie Sheen? Come on! I laughed, giggled and guffawed my way through last week's highly irreverent Two and a Half Men Christmas episode. I'm beginning to think that the American Family Association, the organization that has called for an apology from CBS, has no sense of humor.

In the action alert on the AFA's web site, they claim that "CBS and Sheen knew that the lyrics [to Sheen's revised Christmas carol] would greatly offend Christians, but did not hesitate to air them." Somehow, I seriously doubt that these lyrics

“Joy to the world, I’m getting laid; I’m getting laid tonight.
We’ll light the yule log, deck the halls, and then we’ll play some jingle balls.
It’s been a real long wait – this is our second date!
It’s Christmas Eve and I’m getting laid.”

were flagged by Standards and Practices as offensive to Christians... and I think that we all know from watching Studio 60 what Standards and Practices thinks will offend Christians.

If anything from that episode was questionable, it might have been the subplot of Jake, Charlie's ten-year-old nephew, getting wasted on eggnog and throwing up in the car on the way to Grandma's house. I mean, doesn't underage drinking pose a much greater threat to American Family Values than some re engineered Christmas carol!

I guess I don't understand American Family Values at all. If revising Christmas carols and relabeling "Christmas Sales" as "Holiday Sales" are what is really destroying the American family, I think I'll just hole up in the godless city of New York and spike all the minors' drinks at the next Holiday party.

And, for all you other irreverent family values destroyers, here are some alternative lyrics to favorite Christmas carols. Though they're most popular with the 8-10 demographic, I still find them highly amusing. Merry Christkwanzakuh! -Flygal

(to the tune of We Three Kings)

We three kings of Orient are
Smoking on a rubber cigar
It was loaded and exploded

We two kings of Orient are...

(to the tune of Joy to the World)

Joy to the World!
The teacher's dead
We barbecued her head!

What happened to her body?
We flushed it down the potty
And around and around it goes,
And around and around it goes,
And around and around and around it goes!

(to the tune of Deck the Halls)

Douse the halls with gasoline
Fa-la-la-la-la La-la-la-la
Light a match and watch it gleam
Fa-la-la-la-la La-la-la-la
Burn the school house down to ashes
Fa-la-la-la-la La-la-la-la
Aren't you glad you played with matches?
Fa-la-la-la-la La-la-la-la

Jacob's List or Ladder or Something

I'm entertained by the fact that even though Lost is off the air until next year, Jeff Jensen at Entertainment Weekly is still postulating away about where the mythology is going. This week's whacked out theory: the connection to the Old Testament...

I'll admit that the names and the mythology seem to be congruent, and the whole science vs. faith thing seems to fit but I think that it's about as likely that the Others are a lost tribe of Israel as it is those crazy evangelists in Times Square are.

Thoughts?

Heroes: a mid-season entertainment and scientific analysis

The first half of the first season of Heroes has just completed. And I just have to say Wow! and Whew! Never have I been so riveted to a show waiting with baited breath as the talented actors, writers and director delivered high-quality, entertaining, thought-provoking shows from one week to the next.

Well never since I started watching Lost. But this post is about Heroes and will not dissolve into a whiny rant about how much better the first season of Lost was and how the writers have no idea where they're going... you can go to any of the TWOP Lost Forums for that...

I won't attempt to recap last night's episode, Erin over at TWOP has been doing a fine job with that, but just want to offer some commentary on what's known, unknown and the minor annoyances this show has brought me, as a geneticist.

Where we've been
Up to this point most of the episodes have focused the phrase, that I feel compelled to whisper every time I even think about watching an episode of Heroes, "Save the Cheerleader, Save the World!" It was totally creepy when Future-Hiro first announced it to a stunned Peter Petrelli in the frozen NYC subway. (For the record, Peter totally got the evil subway eye from Mohinder for spouting that "but didn't you see him? I mean time just STOPPED, and there way this guy with a sword" crap) And now? Peter has saved the cheerleader, but based on the last 5 minutes of last night's show, he's the bomb (or da bomb!). Which is odd since we've already met Radioactive man, Sprague, who melted his house and gave his wife cancer. Tim Kring has also stated in a TV Guide Interview that "we'll posit another theory that [the nuclear bomb] is Peter [Milo Ventimiglia]." so it's not entirely clear to me whether it's really Peter or Sprague who's da bomb... though Peter's definitely hotter

One refreshing attribute of Heroes remains the transparency with which the shows actors and creators relate to fans and the media. From Greg Grunberg's spoilery interview with Michael Ausiello (follow the link and see video links on the right) to Tim Kring sitting down to talk to various news sources, it's clear that the Heroes writers and cast don't mind revealing plot points ahead of the episode's air date. That keeps the fans (the same ones who are snarkily posting that Lost writers have no direction) happy. Hopefully Kring and cast will continue this practice, since, even though I'm not a snarky fan, it makes me happy too!

What we still don't know
The great thing about Heroes so far is that they're wrapping up some mysteries (Six Months Earlier is a good example) while they introduce others (like who was HRG taking his "marching orders" to keep Sylar alive from?). Also falling into the column of "what we don't know" would be why Sylar didn't immediately break out of his holding cell at the Make-Believe Paper Company. Why did he wait until Eden came to kill him? Did self-preservation motivate him to be super-duper powerful or was he just toying with them all along? Also, why does the Haitian want to keep Claire's memories intact? Does he know that the s**t is going to hit the fan in the form of da bomb or is he just tired of being HMG's mind wipe bitch? Needless to say, there are still plenty of mysteries to be unraveled when the show returns on January 22nd.


Minor annoyances
The geneticist in me (yes, the one that loves fruit flies laying eggs on pennies) has trouble buying the premise that based on mutation(s) in the Heroes' DNA Dr. Chandra Suresh is able to track the heroes down geographically. First of all, this sort of tracking would require access to a massive database containing the sequence of every individual in the world's DNA (or at least a sample of it). No such database currently exists, and even if it did, Suresh would have to obtain prior informed consent from the individuals whose DNA he tests in order to test for the presence of the mutation(s). I might add that such prior informed consent would probably be easy to obtain from Sylar who was determined to be different and special but would likely be difficult to obtain from such reluctant heroes as Nathan Petrelli, Claire Bennett and Sylar's first victim (the telekinetic guy who wanted to get rid of his power to avoid hurting anyone - yea, that didn't turn out so well). The whole question of privacy and mining of DNA databases is a huge ethical issue that policy makers both in the U.S. at NIH and through international organizations such as OECD and WHO are wresting with. It might be interesting for Heroes to give Mohinder a plot line where he has to convince some international organization that free and open access to genetic databases is necessary to preserve the world. At any rate, it would give him something to do besides the annoying voiceovers.

Finally, just a quick eulogy for Eden. Nora Zehetner brought Eden (aka Stinkerbell) from a girl who had defined her own morality through mind control, convincing cops to eat doughnuts rather than arrest her to the hero who helped Issac recover from his heroine addiction and who made the ultimate sacrifice by taking her own life so that Sylar could not obtain her power of persuasion. We'll see you in flashbacks, Eden.

Courtesy of Tombstone Generator

Would you like coffee with your Evil Subway Eye?

On a recent morning as my train crossed the Manhattan Bridge and I gleefully anticipated filling the seat my mark was about to vacate, a small subway drama unfolded across the car.

To set the scene, I was at the end of the car, facing a very "local" man sitting down in the right seat of a two-seater next to the train door. A young hipster was standing next to him drinking a cup of coffee.

I was reading my New Yorker across the car when I suddenly heard the local man exclaim, "Whaddaya think this is a f***ing cafeteria?" The hipster looked like he very much thought that this was definitely not a cafeteria, and that he was about to get his ass kicked. He apologized softly as the local guy mopped the 5 drops of coffee off his shirt. The local guy continued to grumble about how the hipster ruined his shirt (which if you ask me, the coffee stain was an improvement) and flashed the uncomfortable looking hipster the evil subway eye.

You may think at this point that I'm extremely uncaring about the plight of the working man and am an advocate for hipster rights, but you're wrong. I think that hipsters are a next step in the evolution of the annoying girls with big bangs with whom I went to middle school who became the annoying partiers I went to college with who drunkenly pulled the fire alarm at 3 AM on a Sunday morning. I'm a big fan of local Brooklynites, especially the ones who have been there since before Brooklyn became "hip." I love listening in on their conversations at the local laundromat. Their lives are so different from mine, somehow more "real" and less plastic than my own burgeoning yuppie existence.

But in this case, I had to pity the hipster and turn my evil subway eye to the local guy. I mean, really, it's 8:00 in the morning, and we're all a bit annoyed to be schlepping into work. Could you cut the guy some slack? And the subway looks in no way like a cafeteria! I mean is that really the best disparaging remark he could come up with? And seriously, his shirt looked like it was purchased circa 1985 and, as I mentioned above, the coffee was really an improvement.

In my view, you've gotta feel bad to the hipster trying desperately to get his morning caffeine boost so that he can face another day of his youth, knowing all the while that 25 looms like a large gray cloud over his head. That one day, dressing in corduroy pants, plaid shirts, jaunty hats, slouching and badly needing a haircut will no longer be a viable option. That he'll have to grow up, get a haircut and perhaps do something more productive with his Saturday afternoons than hanging out in Williamsburg discussing the greatness of Iron and Wine and experiencing the existential angst that only comes from wearing a jaunty hat and sipping over-priced microbrews.

Though perhaps equally angsty and yet ultimately thrilling was the hipster's nearly-averted early morning ass kicking drama that I observed. Ah, commuting! still better than the Metro red line in DC.

Fix That Data!

Ironically, in the same issue of Science magazine where editor-in-chief Donald Kennedy summarized actions taken by Science to improve its editorial process in the wake of the Korean Human Cloning Scandal, a new scandal has been reported. This time scientists in a Missouri lab allegedly falsified data published in the February 17th issue of Science where they claimed that key cell fate decisions made in the early mouse embryo occur at the very first cell division.

Mah, you may say, so what? So plenty! The determination of anterior-posterior polarity in the embryo is, frankly, what keeps your head out of your ass. Those individuals who choose to realign their body plans later... well that's a personal choice.

The key observation in the February 17th paper was that one of the cells produced in the first cell division of a fertilized mouse egg expresses higher levels of the Cdx2 transcription factor (a class of protein that controls the expression of other proteins) than the other. This initial difference could help explain why certain cells in the mouse embryo are better for generating clones than others.

And now? Not so much. It turns out that the observation that Cdx2 is higher in one mouse cell than the other is fairly easy to fake using Photoshop, or Correl Draw or any of the other common tools embryologists use to prepare their microscopic images for publication. This is not only unrepresentative of the actual data but also tantamount to lying about the results.

Falsification of data is wrong. It's also pretty dumb since the first thing that competing labs do once a paper is published is to try to replicate the results. If they can't get the experiment to work, and they're a hot shot lab themselves, the fraud will be uncovered pretty quickly.

But even if uncovered expeditiously, the cost of fraud is great: in the time of the reviewers, the time of the journal editors, the time of the scientists both perpetrating the fraud and uncovering the fraud. And when you're an academic researcher, the tax payers are footing the bill for all of that time.

So who bears the responsibility for scientific misconduct, as the policy wonks are calling it? With the exception of Woo Suk Hwang's very public denouncement by the global scientific community, it's generally not the lab head, or as they are called on grants, the Principle Investigator (PI). Generally, the blame falls on lower level scientists, often postdoctoral fellows (PhD scientists in an apprenticeship position with the PI) or in some cases the graduate student pursuing a PhD with the PI.

These lower level scientists often carry out the experimentation and are in direct contact with the data. However, a laboratory is led by the PI and there should be some accountability by the management of the lab for transgressions that happen within it. The PI's name is on the grants and is generally the last author on the peer-reviewed publications, and thus should be held accountable.

So why is this not a common practice?

It's no secret that PI's are given little, if any guidance on how to run a lab. Most are thrust from their positions as postdoctoral fellows directly into positions as a lab heads. They receive little mentoring, and no management training as if running a lab were as instinctive as flying south for the winter. Some inroads have been made to this problem, such as the Howard Hughes Medical Institute Guide to Scientific Management and the UC Davis Laboratory Management Institute but management training should become a more mainstream part of scientists career development. (If you think that ANY career development would be an improvement over what they've got now, I'm with ya!)

Perhaps with better management practices in place, including frequent meetings and structured oversight of lower level scientists, misconduct would be less easily hidden from the PI's. And perhaps fewer PI's would suffer from the anterior-posterior realignment to which I referred earlier.