Shut up

If there is one thing that hasn't changed in the lab, it's the presence of Bunny. You know the type of person who just has to strike up a conversation with you. They would rather talk than sit through silence. It's tiring to come up with something to say to her, to converse about, because you know, my life isn't all that exciting. I get up, go to work, come home, eat, sleep.

Anyway, Bunny has to talk. All the time. Even when you indulge her in a conversation in the morning, she has to ask you how things are straight after lunch. Often, I don't have anything to say to her, so I do the old trick of reversing the situation and asking her about herself.

As she likes talking, she knows a lot of people - hence she has a lot of gossipy information. Which is okay, I enjoy listening to that kind of stuff, becaues it gives me more info (however tainted) to judge and understand certain situations.
The problem with Bunny, is that often, her output is flawed. She might say certain things about certain institutions, certain PIs, etc., but you can only really believe a part of it. I haven't figured out whether it is because she is shortsighted, she doesn't have the whole information, or just misinterpretation (and when it involves her, the she always plays victim). But certain things are so obvious to me, that you wonder what she believes and where she gets the information.

This was made apparent when she was talking about her Ph.D. supervisor a while ago. She has always had an....antagonistic relationship with her supervisor, and I think it is a two way thing. She has an attitude problem, and he's a piece of shit. Not a good combo.
Anyway, so throughout the years, we in the lab have been bombarded by her comments and complaints and whinging about him. And then suddenly, a few months ago when I asked her how her thesis was coming along, she was sympathetic to him - even defending him when I slagged him off (which I thought would make her happy, since there was an ally listening to her). Then now, it has reverted back to "he's a piece of shit" attitude.
Which makes you think.

I'm all for changing minds, and evolving ideas. But this change was uncharacteristic to say the least, that it kinda surprised me. What did he do to make her change her mind, even for a few days? It must have been one hell of a carrot he was dangling in front of her (ugh, that just sounds so wrong!).

Bunny didn't explain the carrot to me at least, so I am left with a little confusion and a fair amount of mistrust in her words.


BTW, I figure that this lack of talkativeness from my part partly stems from the fact that almost everything is under control - I have no reason to fret and complain and whinge at the moment. I feel okay, no problems, so I don't need to vent. Yet.

Publications

I was reading stuff over at DrugMonkey, and thinking about this desire to get a C/N/S paper (I did snigger at that, the sad, sad state of my sense of humour being what it is - since I'm not working in brains, I am going to use CNS instead of using all the slash).

Coming from a cellular/molecular biology 1st postdoc, I agreed about getting a good quality paper in CNS. But as my 2nd postdoc is in a more medically related field, my thoughts have changed a bit over the last few years. Hmmm, maybe it's maturity. Or giving up on the career highway.

I've had a chat about this with several other people, all from differing fields. We all agree that it is hard to get a publication in the CNS. But the fact that they have a wide readership makes it difficult to publish in it. In my particular field, I do see very occasional papers in the CNS, but it is very very rare now. I think my field had its share of "defining" papers a decade or more ago, and it is rare now to see such papers in CNS journals. Also, my field is relatively well-developed (i.e. has been around a while).

People in my field, I think, tend to go for specialist journals, and I think that in part, it is due to the nature of my field - it straddles between medicine and molecular biology, with a strong slant towards medicine.
I also think (maybe wrongly) that it can be difficult to "justify" the science to non-specialist audiences - I feel like you really need to show a really interesting phenomenon, which has a real impact on the future of humankind, to get a CNS publication (ok, N and S at least).

Being more involved in the clinical possibilities also made me question about this desire to publish in a well publicised, high impact factor (IF) journal. There are other, highly regarded, high-ish IF journals out there. It's just that in our little field, that high-ish IF tends to top at around 8 or something, and rapidly decline to the 4's, 3's and 2's.
Having said all that, I am not applying for PI positions, so I am not under a lot of pressure in that way.

The other thing is, me being who I am, love gossip. So for example, I would love to know that Dr.X's Nature publication only came about because he is chummy with the editor. Or that Dr.Y's Cell publication only came about because he hassled the editor to death. Or that Dr.Z's publication only came about because she is the editor's ex-postdoc, etc. etc.
It doesn't help me in anyway for me to get my CNS paper, but I kinda like to hear things like that. It's funny.

On an aside, I remember presenting a paper for journal club, which I picked because of the title and abstract. Ok, and I admit that the well known PI's name as last author helped too. I hadn't really read it, and when I studied it carefully, I was absolutely appalled at the quality of work (not to mention English) - I was ashamed to have chosen it. And this was published in a "high IF journal" in our field.
After going through the paper, one of the PIs at the journal club pointed out that the last author had been the editor-in-chief of that publication (but wasn't at the time the paper was published). So it makes me think, you know, small-ish field, everyone knows everyone....maybe someone owed someone a favour? And you don't want to get in the bad books of the bigwigs.

That's humanity for you.


BTW, I just realised that I am assuming that CNS stands for Cell, Nature and Science, and not the related journals within Cell Press or NPG. Science doesn't have sister journals does it? And I was kinda surprised that Cell Press now does the Trends series. How things change...

Give it back! Now!!

Between being exhausted after work and sleeping, I haven't really been keeping up to date with all the bloggage available. However, I did notice the new people post over at PropterDoc, which reminded me of my current predicament.

While I was gone to JSA-land, my boss had kindly kept my desk and lab space in our office and lab. That is no mean feat, when our lab is like a garden full of dandelion (a.k.a. weeds), whereby when one person leaves, before anyone can say anything, the space is taken over by another person. It's like the African plains, those hyenas looking around for any opportunity to pick a carcass.
It's just that there are so many people working in a limited space, and it is amazing how PIs forget to mention they are bringing in new undergrad/MSc project students for 10 weeks/2 months/half a year. I think that the PIs think these project students are temporary and that they can imagine doing experiments rather than doing them on an actual, physical bench.

Anyway, so my bench is still there, but lacking things like pens, scissors, my box of razor blades, tips...fine. I can get them again. But then, we have this undergrad project student who is here for 10 weeks, who had been using my bench space. That's okay. He moved to another bench.

But he took my set of Gilsons with him.

And he labelled it with his initials.

He is not on my "favourite people" list at the moment.

Granted, it probably isn't his fault. But I have to get my Gilsons back, I need them. At the moment, I am using Doc's set, because he is never at his bench when I am there.

But the fact that I have seen him use my Gilsons, means I have to clean the barrels. I don't think he has been doing bug work with them, but I don't trust him. He's an undergrad student after all, and he might even be from Medicine, shock horror.
(BTW, I use filtered tips for bug work - as in, inoculating and plasmid preps - because I don't trust myself, and it's better to be safe than be sorry when you are using the same Gilson for bug AND DNA work.)

I wonder what's the best way to go about getting my lovelies back. I hadn't started working yet when he was (presumably) introduced to the lab. He probably doesn't even know me (well, we haven't been officially introduced). It feels weird and unwelcoming to go up to a person much junior than myself, and demand to get back my Gilsons.
And to interrogate him as to whether he used them for bug work...
And to scrupulously clean all the barrels...
And to rub off his initials...

Tired...

It's lovely to be back at work, but I am physically quite exhausted. My good few months of rest has made me a thoroughly lazy individual (some may say I already was), and it's quite taxing to be running around all day trying to sort stuff out.

Speaking of which, one of the stuff I did talk to my boss about was the DMSO. To which his gung-ho reply was to dissolve the compounds with whatever DMSO we had (which would be the old 100 ml bottle in the tissue culture room, which has been around since at least 3 years ago). The conversation was something like this:

Me: "I was wondering about the DMSO..."
Boss: "I thought about that. I think the last time we had to dissolve it, we just used the one we already had, and I think it was okay. Yes, it was."
Me: "Do you think that's ok, since you did talk about stability issues..."
Boss: ".......oh, I'm sure it'll be okay, just do it"
Me: ".............I guess I could ask the chemists about the stability towards water......"

Like I'm going to listen to that! I already ordered some DMSO ampoules from Sigma, and I am waiting for that to arrive.
(In the end, as SuperTech and myself couldn't decide on a good drying method before my post below, so we decided for the time being to buy (what I hope and think is) anhydrous DMSO in 10ml ampoules. I had used them before for tissue culture purposes - they are specifically for t.c. use. At least it will be dry, will be sealed until we break it, and we don't have to worry about dessicants.)

There were other things, like
"is it wise to use plastic tubes to send samples in - not because of DMSO per se, but more because the compounds could adhere to plastic"
and
"should I be doing all these experiments before I did the restriction digest of the plasmids",
answers to all of which were "just do it and see". Which makes me a bit nervous, but hey, he's the boss.

I also know that he is under a bit of pressure with my project already - the time it has taken to actually get me employed, was far longer than anyone anticipated - so I do understand the anxiety.
For the time being, I will be doing what he wants, as well as keeping an eye on everything else - God knows I don't want to be using the wrong bloody plasmids for half a year before realising it.


The other thing that is irritating me has nothing to do with the actual science or lab, more to do with infrastructure of our building. Our building has one of those swipe card systems, so to get access to certain rooms, you need "security clearance". All nice and fair, if the security system is up to scratch.
I went to get my card activated for access to our tissue culture room, which happens to be housed inside a card-only corridor. Everyone was happy to grant me access, except for the system. They registered my card, but between the terminal at the reception and the card swipe machine a few floors up, data is not travelling. If it is, it's on the back of a tortoise.
It's a system fault, so they have to get an engineer (I guess from the company who installed the system) out to fix it. Apparently, the engineer came on Wednesday, disappeared, and has not returned. Maybe he was kidnapped by aliens. Not.

The thing is, I need access to that damned corridor. And I needed it yesterday. It's so frustrating when something like this prevents you from work. It's extra hassle to keep on trying my card on that damned door, going to pester the receptionist...it's totally unnecessary and a waste of my time.

Gotta love

I went to see The Black Keys recently, and as they are touring their new album, "Attack & Release", I thought I'd give them a shout here. Those of you across the pond, as well as those of you in Oceania can still catch them in the summer.

I've got all their albums, but the ones I like most are the 1st, 2nd ("The Big Come Up" and "Thickfreakness" respectively). However, they did have a song used in a car advert over here.
At the gig, they played a selection of songs from all albums (like "I'll be your man" from the 1st), which was great, because I don't particularly listen to Rubber Factory (3rd) or Magic Potion (4th).

I do like bands with either a minimal setting. 'Tis a shame that Death From Above 1979 (they were a bassist and a drummer) are no more. I would have loved to see them live.

DMSO question

There was a post recently over in In the Pipeline regarding my favourite solvent, but my query came late, so I am posting it here.

I have a question - how do people keep DMSO dry (short of distillation)?

An explanation. Well, DMSO is my favourite solvent to dissolve those big MW compounds that I need to get into cells. And ordinarily, I wouldn't really care whether it was in water-saturated DMSO, since I know the stability of the compound that I would be dissolving it in. These compounds I normally use have been around a while.

However, I have a few compounds I need to test. They are novel organic compounds, and I have no idea as to their stability in DMSO, or specifically DMSO which might contain loadsa water. I could revise my chemistry and bond strength and the sort, but maybe I should play safe and keep water away. And the last time I seriously thought about bond strength was over a decade ago. (Hell, I had to look up pyridine on the internet when I saw a benzene ring with a nitrogen in it. At least I could still tell it was a benzene ring.)

I know DMSO is highly hygroscopic, but do people store it in dessicators? I know you can put molecular sieves straight in, but as I will be using them to treat cell-lines, the less crap the better.
And do you use silica gel as a dessicant, or something stronger? I don't really want to re-visit my chemistry days and use phosphorus pentoxide as a dessicant. I think the Health and Safety officer of my lab might die of a heart attack, knowing his reaction after his discovery of a fair quantity of picric acid in our lab (picric acid is used in tissue fixation in histology).

Curse of the plasmids

So today, I streaked out some bugs from a glycerol stock on plates, and also inoculated them for an overnight culture. I thought I'd cover all the bases, just in case the wire loop was too hot when I dunked it in the glycerol stocks and killed the bugs in the process.
...okay, so not only did I probably leave the wire too hot, I also dug the loop into the agar plates. That probably happened because I skimped on the amount of agar. That happened because I forgot the percentage to use. And also, plastic spreaders are quite gentle, and I always used that. Oh well, you only learn from your mistakes. Hah hah hah!!!

I also got 4 plasmids from 2 different people in our group, to grow up. So in all, there are 5 overnight cultures and 9 plates for me to take care of tomorrow, of which I think a third will fail to grow (and I think I know which third...).
If there are colonies, then next week will be my mini-prep and digest week. Hopefully by the end of it, I would have a good stock after maxi-prepping them all. I could get my (who am I kidding? our) supertech to do that, but I haven't really got much going on at the moment, so might as well do it myself.

Why so many?
Well, the 4 plasmids I got, and the 4 from the glycerol stocks, are supposed to be the same. It's just that I don't want any surprises when it comes to plasmids, and that is one thing you learn fast in a molecular biology lab - check, double check and triple check plasmids.

Especially when I am dealing with one that has been around since the turn of the century (ha ha). Or longer. In my course of tracking them down, I have heard three different names for the same thing, depending on the person. Oh, and that includes the presumed original name, the name that was published in a paper.

You would think that a simple reporter plasmid won't be that hard, right? Heh.

The worst case of mistakes in plasmid nomenclature actually occured in our lab, when someone made the mistake of changing the δ for specifying an isoform, and wrote Δ instead. Which everyone should know that it stands for deletion. It made it worse that we do work with deleted mutants, and hence was followed by immense confusion...
Thank God I don't work with that gene.

My first day

This work thing is so over-rated.
I'm shattered.
Dunno how I am going to survive until the end of the week...

Apart from all that, I made some LB broth, LB plates (with Ampicillin), pipetted some plasmids, bought stuff worth over 2000 pounds with my new grant, and read some review article. Well done, me.

My first meeting

So I went in to work today, just for a short meeting. I did my first PubMed search in...a long time, I even looked at the Science website! Wow.

Next Tuesday, after the Bank Holiday, I will start working. I wonder if I can stay up for the whole day. I've been taking naps, and it does become a habit...but on the other hand, I won't be able to stay awake past midnight (like I normally do).
Well, I am off to enjoy my last weekend of freedom. Oh yeah, and better get the P45 form sorted out too.

I will survive

Actually, I'm not sure if I will. I mean, I've been sleeping like a sloth (although I hear that they aren't as lazy as we make them to be), doing nothing all day, what, for 8 months?

I'm starting my job next week.
Aw, hell.

Anyway, hence the change to the top blurb about my blog. I shall once again become a postdoc. Wow. If I make it to the end of this, that would be an 8-year career as a lab monkey.

Interviews

At long last, I might be back to the land of taxpayers.

Yes, I have applied for a position - the position I was eyeing for the last few months. With my last supervisor. The grant came through, the ad went out; I applied, and I had an interview.
See, I'm superstitious, and I had the interview on Tuesday, but I didn't want to jinx it, so I'm only writing about it now.

It's so hard to be motivated to write a presentation (10 minute short, too) which you will be doing in front of your old boss, about the work which you and your boss are writing a paper about.
And a paper which has been such a pain in the ass that you'll be happy seeing it published, if only to get it off your IN/OUT tray. I mean, are we not sick of this work yet? Have I seen these figures, like, 100 times before? And how do you distil a 10-page paper worth of work into 10 minutes? Talk real fast?

It's even more of a motivatory problem when you know the person you are interviewing with. Granted, I don't know the other person in the "interview panel", but still, I can hazard a guess as to which of the busy/lazy PIs will be interviewing me (as in, who is too busy, who is too lazy, and that leaves who).

It's a funny thing when you are the internal candidate. In my case, as the grant hadn't come through quick enough, I am applying as an external candidate - I think it is because for them to employ yours truly, they have to do it by the book and just go through the whole process - but all things considered, it makes sense to employ me. Of course, I am not counting chickens until I get my official letter, and I am not going to be that peeved off if I don't get the position - I think I'll be more relieved that now, I can REALLY start looking for a job.

Whilst I was talking to our SuperTech (apres-interview), Mr.Strauss kind of mentioned that "it must be hard when you apply for a position when there is already an internal candidate". Which is true. But for those of you who are sceptical about applying for such a position, think about the positive.
It will be an exercise in interview techniques. You will get practice with different interview methods. You will practice your talk. You will get reimbursed for your efforts. If you do make an impact, at least you know the other person knows you (a kind of "getting your name known" exercise). And anyway, you AREN'T supposed to know that there is an internal candidate.
Granted, it's trying to make you feel better when there is not much of a chance of getting the job - but why look at the doom and gloom, when you can scrape the bottom of the barrel for a little hope?

And I tell you why, despite being the internal top candidate, I am still unsure - because one of my friends actually got a position whereby he was an external candidate, applying for a position where there was another person lined up for the position.
When you hear something like that, you make sure before you go an plan the future. And it probably also is because I am really suspicious and don't trust easily. And of course, you never know.

It might be that the interviewer (PI) meets the woman of his dream and wants her to get the job. You never know.

Gifts - Two

My boyfriend went to a conference, and all I got was this...




No, not the fridge magnets on either side of the "Y". The "Y" is what I received. As you can probably guess, it is a PR magnet for Erbitux. Obviously, it is an antibody. That Y-shape is such a dead giveaway really. Just in case you were unsure, it even tells you that it is an IgG1 antibody. Gotta get the science right.
It's a pretty big thing for a fridge magnet, and quite heavy too. To give you an idea, the Sainsbury fridge magnet on the left is 7cm by 5cm (at the widest and highest points). Yes, the "Y" is humongous. I think you can kill a mouse using this orange contraption. It really is heavy for a fridge magnet. It is 125 grams. I am still amazed at the strength of the magnet used. The Y doesn't slowly slide down the fridge door, as I would suspect will happen if the magnet is not strong enough. I bet that magnet added a bit to the cost of production (of this freebee).

When I got this, I thought it really was something else - I think I received it in a box, and you know, from the dimentions and the weight, I never would have guessed it was a freebee, or a fridge magnet, or a magnet in the shape on an antibody. Wonders never cease...

Gifts - One

So as those t-shirts say, "My boyfriend went to a conference and all I got was this..."




Meet Ducky. The military rubber duck, 5cm high.

RTS

What does RTS stand for?
"Return to Sender", of course.

It started innocuously, when one envelope from a division of the national broadcaster was sent to my humble abode. It was addressed to an unknown male - Mr.X shall we say - who I had no pleasure of knowing. So I sent it back, with the address crossed out, written "Return to sender" in black ink. You know, so that they won't make the mistake of sending the same thing again.

I even got a visit from this Mr.X a few weeks ago. He apparently lives on the same road as me. He assured me then that he had corrected the mistake, and that no more mail will come my way (and that if I had, or ever get any more of his mail, to give it to him. I didn't, since, like a good citizen, I had sent the said mail back through the mail box with RTS on them. And I haven't bothered walking to his place to give him his mail, because (a) I am not wasting my energy on walking 20 metres to deliver someone else's mail, (b) I don't get paid to do it, and (c) I forgot which house number he actually lives in).
I think he has really bad handwriting when it comes to numbers. He must do, since either (1) they couldn't read the address properly, and/or (2) the person putting it in the database made a mistake in reading it.

One month later, I still get the mail for this Mr.X through my letterbox. BTW, this is, like, after a dozen letters have been sent back to them with the RTS.

I am beginning to think that these people really like wasting my time. And the licence-fee payers' money. And possibly my energy (of writing the RTS on the envelope). And my money (gimme back my ink).
Most companies actually do something when they send the wrong stuff to the wrong people. You know, like, amend the details. I think in this case, since Mr.X seems to still work for this particular division, they keep on sending it out. To the wrong address.

I mean, if I was Mr.X, I'd be worried. According to the meagre details on the envelope, the contents of the said envelope seem to involve money (as in pensions contributions, and pay). I guess it is just a letter of confirmation - I doubt anyone pays anyone by cheques through the mail anymore, when you can just do a quick transfer through BACS. And just last week, I got another mail from what I think is the pension scheme company that he is part of - the envelope had a different name for the sendee. Which means that whatever Mr.X's employer is doing, the one thing they haven't done is amended their records.

Which is not my problem.


However, I did wonder about putting some profanity laden message on the next piece of mail that comes through my letterbox addressed to Mr.X, as in:

"Return to sender. ******* addressee doesn't ******* live here. Never ******* has. So can you ********* stop sending your ******* mail to me. It is wasting everyone's ******** time. If I wasn't so morally uptight and proper, I will ******** ******** ***** the next piece of ****** you send me.
Yours sincerely, the suffering occupant of this address"

Vanity and gayness

Recently, I was introduced to this interesting Stateside "anthropological phenomena" called the "Guido". It all started with a viral email, which was followed up by URLs of several sites, including GuidoFistpump (which, to me, sounds like some gay porn site) and a definition of a Guido by a Cajun Boy in the City.
I guess it is similar to the Chav phenomenon over here, except that the chavs aren't (by definition) rich. Maybe the current Guido is the evolved version of an equivalent chav phenomenon. BTW, I personally don't think the wiki entry does justice to the chav, if that makes sense or if it is possible ever to justify a chav.

Anyway, after going through some websites, I started thinking. All this Guido-ness: the simple beat of the club music, the dancing, the vanity displayed, the bulging muscles, the hairstyle......if I saw one of them in England, I would think they were gay. Seriously. Because that is the gay sterotypes you see in, ur, gay clubs, over here.
Not the orangyness and the fake tan, mind you, that (according to sources) was more a mid-80's thing. Having said that, you do see orangyness over here too, but I don't really see a direct positive correlation of orangyness with chav-ness.

I guess the difference in perception arises from the fact that a Guido is a descendent of Italians (-American working class). The suave Italian male image doesn't translate at all to English /British culture. So while the current Guidos, despite their similarity with the chavs, are totally hetero (I assume), the equivalent... male example over here, might be stereotyped (at least by me) as being gay.

Interesting.
And yes, you can guess that I am running out of interesting topics to write about.