Oh did you notice this blog has been quiet?

For a while I was posting on MySpace, but now I'm over on my own host.
Check out the new pad over at Todayland

It's in God's hands

My wife was watching Dateline last night, and I was too lazy to get up and walk away. They were doing a story on conjoined twins that were undergoing separation surgery. The most ironic part of the story was a point where the babies are about to go into surgery, and the parents say something to the effect of "I trust in God, it's in his hands now", to which I replied "well he sort of screwed it up the first time around, eh?"

Honestly, it astounds me that people believe that an all-knowing "Intelligent Designer" would create something like conjoined twins. This seems like a problem that would be engineered out pretty early on, right? If there were a God, I think it would have probably been easier for him to just make the twins in the normal way, rather then putting the parents through the agony/suspense, and placing these two babies in such mortal peril.

I am born under the sign of "boned"

Ok, I have come to the conclusion that I am cursed as a bench scientist. I know how to do the work, but despite my best efforts, something goes wrong at every turn. I know that the other scientists out there might be saying "that happens to all of us", but I would argue that it's worse for me than for you. As evidence, I submit my protein refolding protocol:
The protocol steps are listed below, with sub-bullets indicating the way these have gone wrong over the past 3 runs

• The protein expresses to inclusion bodies, so first you have to isolate the inclusion bodies by resuspending in buffer + detergent several times, sonicating to rupture the cells, and centrifuging to collect the solid bits with your protein still inside
• During this step I've managed to cross-thread both a centrifuge bottle and the centrifuge rotor. Didn't lose anything because of this, but it was not easy to retrieve the sample
• Next you resuspend the inclusion bodies and add a reagent to modify the cysteines.
• Time will tell if this has gone wrong or not, but today the sample kept going from orange to clear, which it's never done before (usually it stays orange). I would add more reagent, but it cleared back up...
• Ok, then you dialyze the protein against dilute acetic acid
• I've had dialysis bags break, spilled the acetic acid on myself, and had to use the wrong sized tubing because we're out of the right kind
• Next you pellet the precipitate and lyophilize (dry) it
  
• Haha, the first time it wouldn't pellet, so I collected the precipitate using a Buchner funnel and then scraped the protein off of the filter. Even when I do get it to pellet, we don't have a large enough lyophilization jar to hold the centrifuge bottle, so I have to scrape it into a conical again, undoubtedly losing some
• Ok, now you resuspend the lyophilized protein in buffer and dilute it to start refolding
• The first time I tried this, all of my protein precipitated. The next time, the beaker that had the protein in it fell off of the stir plate. The next time went ok, but...
• Next is to rotovap off the Acetonitrile in the buffer above
• The organic lab's rotovap wasn't working, so I tried to evaporate the acetonitrile with a stream of nitrogen
• Next you concentrate it down
• Our concentrator is missing a part. The replacement part is on backorder

FSM help me when I get to purification...

PZ is a genius

Pharyngula has one of the best blog ideas ever running over there at the moment.
I could think about the answers for DAYS
Here are my answers to his example questions:

1. My favorite body part is/are my thumbs. Those things are just fantastic
2. It's EEE-gor
3. Science doesn't help in the bedroom, it actually tends to get in the way (analytical thinking and scientific method always seems to kill the mood)
4. Real Genius is the best interpretation of grad school I've ever seen
   
5. Oh man, I wish my skin expressed GFP. That would be so much fun whenever you went past a blacklight
6. Not really a question
7. I like listening to Kanye West's "College Dropout" album at work
8. I'm not really sure what he means there

Anyway, make sure to check out the comments as well, they are fantastic

Counseling

So I started going to counseling yesterday for a phobia that I've had for about 7 years. I'm not ready to go into the details here, but suffice to say that it's been negatively influencing me for some time.

It was my first foray into psychological counseling, and I have to say that it wasn't exactly what I expected. It was emotionally hard to open up to a total stranger, but at the same time a bit liberating. I think that what really helped was that the counselor was very understanding, and didn't act like I was completely bonkers for having an irrational fear.

Hopefully it will work... There are a few treatment options. I'll post more as everything progresses

PCR is my nemesis

For the past few weeks I've been beating my head against a wall trying to do a point-mutation PCR. For those who don't know, this involves a pretty basic procedure where you have a template bit of DNA that you'd like to copy, the machinery to copy DNA, and some small primers that tell the machinery where to get started. This reaction has been one of the backbones of DNA work for a while, and is pretty much "Cookbook" (i.e. just follow the recipe).

Well for some reason mine isn't working.

I've never had a ton of luck with mutagenesis, and I'm not really sure why. As far as I can tell, I'm doing everything right, but I just don't get any product. When I do, it's not what I want... Very frustrating.

At least I've got protein expression to keep me occupied, and E3 coverage to check out in my spare time.

MMORPG + FPS = MMOFPS?

Webzen has brought together the MMORPG and the FPS into an MMOFPS

read more | digg story


This game looks like it has some potential. Supposedly there is going to be a playable demo at E3, so I'm sure we'll be able to read some previews at that point.

I've tried to stay away from WoW, but this sort of game could be very bad for my free time/wallet

HAH, even the Vatican doesn't believe in Creationism

http://news.scotsman.com/international.cfm?id=674042006

BELIEVING that God created the universe in six days is a form of superstitious paganism, the Vatican astronomer Guy Consolmagno claimed yesterday.

Brother Consolmagno, who works in a Vatican observatory in Arizona and as curator of the Vatican meteorite collection in Italy, said a "destructive myth" had developed in modern society that religion and science were competing ideologies.
He described creationism, whose supporters want it taught in schools alongside evolution, as a "kind of paganism" because it harked back to the days of "nature gods" who were responsible for natural events

One of the dumbest (or funniest) things I've ever seen

I was reading this article over at Nobel Intent, and for some reason scrolled down to the comments. I've been trying to avoid this lately, since there is always way too much ID Creationism in these comments to allow me to avoid spewing my lunch.

The winner for this thread (only 3 comments in!):

Posted May 03, 2006 @ 1:24PM by Chazz

How can anyone not say that clasic evolution is flawed in comparison to a theory of directed species alteration and change?

Evolution is energy-intensive and extremely wasteful when set side-by-side with some guys in the lab that make a couple genomic changes and insert the altered nucleus into an egg that then gets implanted. Both can accomplish the same objective but the lab version will take place many orders of magnitude faster and more efficiently. Now replace "guys in lab" with "unprovable supernatural force with unlimited powers of observation, cognition and manipulation".

Does this make evolution a non-valid theory of how life changes in reality (yes, aside from the clearly liberal bias that reality favors)?

Wow, unless this is satire, that has to be one of the more absurd things I've ever seen. Ok Chazz, even though that statement hardly merits a response, here goes.

My only hope is that the inclusion of the phrase "liberal bias reality favors" is from the performence by Colbert at the White House Correspondent's Dinner, indicating that your post is satire.

There are all sorts of bits to pick apart here, but maybe the easiest thing to point out is this: One of the really powerful, recent develoments in molecular biology is a technique called "directed evolution", where instead of making specific changes to an organism, a scientist simply puts a large population under a carefully chosen stressor, then selects individuals that perform well under this stress. Iterate a few (hundred, maybe) times, and you get an organism that does fantastically well in conditions that were impossible a few generations before. If you then pull out the DNA, you find out that you've got mutations in some key places.

What we have here is evolution doing something that "some guys in a lab" making specific changes couldn't do in a very long time, indicating that evolution really works, and in some instances is much more efficient than fully "rational" experiments.

Oh, and I can't help but note that you claim evolution is "flawed", then put forth a hypothesis with the words "unprovable", "supernatural", and "unlimited powers" as less flawed. Good job. Got to be satire...

Meet the Geeks

Seed has a pretty interesting interview with Al Jean from the Simpsons and David X. Cohen from Futurama.
http://www.seedmagazine.com/news/2006/05/meet_the_geeks.php

I didn't realize there was so many scientists writing for the shows. I guess I always thought that the writers were "recreational" scientists, not actually trained. Maybe that explains why both shows are so damned funny. I'm really looking forward to the return of Futurama, a show that I totally missed the first time around. Thank Cthulhu for Adult Swim.

Gaming hardware upgrade 06

I've got an article up on gaming hardware upgrading for 2006 into 2007. Check it out over at HardwareHell:
http://hardware.gamershell.com/articles/gaming_hardware_06/

In other news, we had a pretty fun party at my place over the weekend. The tap we got from the liquor store was pretty bad, causing everyone to think the keg was empty when it indeed was not. Now I've got to figure out what to do with about 2 gallons of warm keg beer. MMmmmmm... warm keg beer.