Guesswork Science

[bronwynrh]

I suppose that most of science is guesswork, really. A hypothesis is, after all, just a glorified, educated guess. Some things, though, we should be able to count on.

When I stained my protein gel yesterday, I followed the protocol precisely and got beautiful results. No really, it looked rather pretty, what with all the aquamarine-colored bands. The protocol then told me to put the gel in a different solution - one that would clear up any background ickiness (not that I saw any) and it would intensify the stain (great!). The protocol also says that this solution will maintain the gel and its stain for at least 2 months. Fantastic, said I, as I changed the solution and left the whole kit and caboodle to stew overnight.

I came in this morning, excited to take a picture of my pretty little gel.

I open the box. . . nothing.

ARGH!

Peiwei witnessed the beautiferous gel, so at least there's someone to back me up, but damn!

So this is where the scientific guesswork begins. I thought about the reaction that occurred to produce the stain in the first place, and thought about how I could reverse the process - maybe reset the system, so to speak. I just tried it out, totally guessing at volumes and incubation times, and am going through the first process all over again. I hope this is a sort of thing that can be reset. I want my pretty blue bands back!

Biology by guesswork is one thing, but chemistry by guesswork is another matter entirely. I haven't asphyxiated myself or my coworkers (yet), so at least I'm not a dangerous chemist. Let's just hope I am a successful one.

On an unrelated note: what kind of asshat puts their dog out at 6am so it can start barking the neighborhood awake? The stupid thing was tied up in its backyard, just adjacent to the bedroom window where I was - emphasis on was - peacefully snoozing. Bastards.

Comments

[kendokamel.livejournal.com]

Did you throw something at it?

[bramey.livejournal.com]

No, I didn't want to be seen or heard 'abusing' a neighbor's dog. Especially since they aren't MY neighbors. I did bang on the window, but it only stopped it for a minute or two.

Oh well. I'm leaving in a couple of hours, so it's no longer my problem :)

[dburr13.livejournal.com]

my neigbors have several dogs that they keep ties up in their yard...and yes...they like to bark.

[wog.livejournal.com]

Remember those airsoft guns I told you about?

Yeah. About $30 would solve that problem.

Nothing like a little (mostly) harmless negative reinforcement. I can see it now..

Yay! I'm outside! What do I do now? I know, I'll bark at that window!
Bark! Bark!
*pop!* *pitp*
WHAT THE CRAP WAS THAT?!
(Dog hides, silent until the next day...)

Remember that they don't even travel fast enough to break skin or bruise, it would just scare the bejebus out of him.

Muahahahahaaa!

[bramey.livejournal.com]

I'll remember that next time I'm living near an obnoxious dog. They don't leave any evidence, do they?

Re: Muahahahahaaa!

[wog.livejournal.com]

Well, there's little blue pellets, but if the dog is less than 100ft away, you should be able peg him on your first or second shot. Maybe there's biodegradable pellets? Maybe you could make ice pellets?

Again, they're not *that* powerful, so if it's a bigger or stupider dog, they may not care. The intention is to startle.

Ice pellets gives me an idea tho... just use chunks of crushed ice in a slingshot!

Man, I feel evil today.

[repoman.livejournal.com]

They should stop calling you people scientists and use "nature detective". Call it for what it is...

Oh, and the guy who would leave his dog out that early in the morning is probably the same guy who was cutting me off while driving on Saturday morning...

[bramey.livejournal.com]

Nature detective, huh? I like it. Can I get a tweedy hat and a pipe to go with the title?

[repoman.livejournal.com]

UPS don't fail me now...

[platofish.livejournal.com]

If its a regular SDS-PAGE gel, you can simply restain it, to bring it back to its former glory!

/geekout

[bramey.livejournal.com]

Ah, see, you I can tell this to!

I was doing a heme (or, for you, haem) stain on an SDS-PAGE gel of my membrane preps. You add the TMBZ reagent, it binds to the cytochromes, then you oxidize the whole thing with peroxide to see the stain. It was gorgeous.

The protocol said to transfer the gel to an isopropanol/NaAcetate buffer to remove excess TMBZ and to enhance the stain - and for long-term storage. Instead, it removed the stain completely.

What I tried to do was reduce the gel again with 2-mercaptoethanol (this was where the guesswork came in) before trying the TMBZ/peroxide again. It didn't work. So either I chose the wrong reductant, or the reaction is irreversible.

I did a regular coomassie stain and got far less interesting results. Not surprising, considering this was just a rough-and-tumble membrane prep. In any case, I still have plenty of samples left, so I can just run it again when I go back to the lab.

It's strange to think I've done all this work, have all this data, only to stop when it gets really cool. Microarrays and 2-D gels are the next obvious steps, but those fun projects will go to Peiwei, the lucky gal.