Life Science Tools of the Trade

Almost every vendor has their version of a Quick Ligation Kit. Most of them end up increasing the cost per ligation substantially. I use old school NEB DNA ligase, the supplied buffer and ligate for 15 minutes at room temperature. Whack your entire 20 microliter ligation into 100 microliters of homemade cells and presto-cheap and efficient cloning. It seems like every new sales rep is trying to sell competent cells. Who buys competent cells when you can make competent cells more or less for free?(message me if you want a detailed simple protocol). Money is always tight but I would rather make my own cells and buy precast gels than vice-versa.

On to the important stuff:
Book: The Guiness Book of Me (a memoir of record) by Steve Church (no, it is not written by Gavrilov, but good guess!)
Music: Thad Cockrell “Warmth and Beauty”
Concert on the horizon: Steve Earle (I wonder if he’ll do “F*ck the FCC” in front of the family friendly NC Art Museum crowd?)
Manuscript on the horizon: hopefully
SAB Longevity Activity: Moderate but increasing.
SAB Laplazard Activity: High, with increasing incoherency (sludge guts anyone?)

Ordering Systems Part II

If Uncle Bob is your idea of heaven, then the third model is Hell. We have the third model at the Made-up Results Council. We are a large organization. There are about 400 scientists on this site (admittedly only a third are actually *active*, but still) and over 3,000 scientists and support staff nationwide (and overseas). Although there are plans to centralize the administrative duties in Swindon (which is second only to Slough in terms of places that seem to exist for no other reason than the British countryside gets embarrassed if there are large, empty spaces next to main roads. On the other hand this happens a lot in Belgium, and if you’ve ever driven there you’ll realize why Europe has chosen Belgium for its battlefield in every major conflict for the past two hundred years), we still have a large contingent on this site.

Admin, which includes purchasing in this sorry tale, are a dark-blooded race of terrifying visage fortunately confined to the deepest, darkest, dungeon-like regions of the old building, ensconced with the Department of Public Safety. When they move to Swindon it is probably too much to hope that Safety go with them. Anyway, when I need to order something (we have an excellent stores system by the way - they stock many everyday items and have an extensive enzyme freezer, but it is impossible for them to stock everything I could ever want without some fundamental rewriting of physical laws) I have to edit a PDF file on my computer and take it down to the trolls in the deepest, darkest etc. Our old-fashioned yet robust orderbook system (two carbon copies - one for our records and one to be returned from Purchasing in acknowledgment) served us well for many years and . . . just *worked*. But this was taken away from us - and there was wailing and gnashing of teeth and promises and threats and impassioned entreaties, ultimately to no avail. We were promised an all-new computerized system, which I have written about elsewhere, that prevented us from ordering anything at all for two sorry months last year and still doesn’t work. The current system is ‘temporary’ until they sort out the crack-headed code monkeys who built the system we’re supposed to be using.

So, we take these order forms downstairs (in duplicate, one for acknowledgment . . .) and leave them in a box where every night a troll emerges from his or her lair and manually enters into their computer what we’ve just entered into our computer and printed out. You see, I just *know* there’s an extra step here somewhere.

Writing this blog you have to wonder who reads this? Apparently quite a few sales managers track the internet comments regarding their sales reps. In honor of this cyber-tracking, I am advocating immediate raises for Tin Lee (Stratagene), Susan Barbee (Roche) and Rob Blackman (ISC BioExpress).
Luckily, I had decided that when I
decided to slam the company and leave the Rep anonymous for poor service and only name the Sales Reps who passed the litmus test (the test being do you run down the hall or duck into a closet to avoid them at all costs).
So if you are googling (not ogling) your sales reps and you see their name posted here. Don’t just give them a pat on the back. Give them a raise. Now.

Weather: Hot enough to fry a d@mn *gg
Music: Alex Chilton “Live in Anders” (The best band you never heard in a Holiday Inn lounge)
Mood o’ meter: excellent
Science meter: above average, preparing to prepare a manuscript in preparation
“Longevity” level on SAB: below average!!!

I have been thinking recently about my previous posts giving reps a hard time about providing pizza, and it getting old. Last week we had a rep (one of our favorites I might add) throw a ice cream party. It was a tremendously nice break from the ordinare. Not only was it timely with the heat wave we’ve been experiencing (103 today folks…115 heat index who hoo!) but the literature was on a back table with some sort of drawing, but no pressure. Everyone was happy, and people actually stayed around and looked at the stuff. No grab and dash for the most part…reps take note…there are ways to keep us around without locking the doors.

Music: anything Steve Earle (concert Aug 27th)
Book: History of the Crusades (don’t remember the author, sorry)
Word of the day: scurrilous (could apply to the forum recently )

I’d like to do a song of great social and political import. The tune should be self-evident. It goes like this:

Oh Lord, won’t you get me a tenured stipend?
My friends all have headships, I must make amends.
Worked hard all my lifetime, no help from my friends,
So Lord, won’t you get me a tenured stipend?

Oh Lord, won’t you write me a paper in Cell?
The reviewing process ain’t going too well.
Nature editors all say “go to hell”;
So Lord, won’t you write me a paper in Cell?

Oh Lord, won’t you clone me this obstinate gene?
PCR fails me, the gels are all clean.
The primary sequence spells something obscene,
Oh Lord, won’t you clone me this obstinate gene?

Everybody!
Oh Lord, won’t you get me a tenured stipend?
My friends all have headships, I must make amends.
Worked hard all my lifetime, no help from my friends,
So Lord, won’t you get me a tenured stipend?

That’s it!

As most of you know I do the ordering for the lab I work in and what I wondered was…how many people out there comparison price shop. Ordering from VWR is the most convenient way for me to order but I’m not sure it’s the most cost effective. I decided as time permits that I am going to compare prices from different companies. If anyone out there knows the ins and outs of different companies or who has the cheapest prices on plastics please let me know. The biggest challenge for me is remembering to take shipping into account!! As I find things out, I’ll let you know. Until then any info or advice you have would be helpful.

It isn’t often that I’ll take a free sample much less use one. I’ve been using the Qiagen clean up kit for PCR products for years and basically it did the job. But……………..
A couple of months ago in walked a new Sales Rep- still wet behind the ears. He gave me a free sample of their SOPE/PCR clean up (www.edgebio.com). I tossed it in the 4 degree and forgot about it. Weeks go by and in walks a sales rep, he has my name and asks me if I had tried the sample. I drew a blank and claimed ignorance. He pulled out a pad with my name and the product sample he gave me. Okay, I was busted-I thought he looked familiar. I promised I’d try it the next time I needed to clean up some PCR products. Being a honest man (most of the time) I gave it a whirl.
Details-
Brief protocol: add the SOPE beads (don’t have a clue what SOPE stands for) to your PCR reaction. Let it sit one minute and spin it through the provided spin column. It desalts/removes protein/primers and dNTPs. No washes, elutions-spin it and you have your sample in the same starting volume your PCR sample was originally in.
Verdict: It works. I ordered a kit of 100. Cheaper than Qiagen. Now I just need to identify a replacement for the overpriced maxiprep kits.

Random Trivia: I once met Cookie (of Cookie and The Cupcakes) on a cross-country Greyhound bus trip. Cookies is often credited with the first nationwide swamp music bayou hit “Mathilda” back in the early 1960s. Cookie passed away a few years ago. Rest in peace.
Irritation of the moment: sucrose gradients.
Music: Son Volt’s “Okemah and the Riot of Melody”.
Summer goal: finally submit a manuscript that has lingered way too long.
Fall goal: posted constant updates on SAB about the progress of the above manuscript.
2006 goals: post number of citations on SAB of the above manuscript one year after publication.
2007 goals: repost announcement on SAB announcing the 2005 manuscript.
2008 goals: repost the total number of citations on SAB of the above mansucript with a year by year breakdown.
2008 goal: fill out the junk mail asking me to join Who’s Who.
DVD : Twilight Zone Volume I (original episodes with Rod Serling)
Cult author: Orville Gonad VI

Remember the bad protein marker story?

I ordered some SuperScript II (not III) on the advice of a post on the Scienceboard. It arrived in timely fashion, but the tube of 0.1M DTT was empty. Not a major problem, but I’ve paid for it so I damn’ well want it. An email to the tame rep resulted in a vacation message, so I called the support line and got them to sort it out. I had to email the order number, etc., and then I got an email from someone else at Invitrogen asking for the same information, and duly replied.

On consecutive days later in the week I received a new SSII kit and a M-MLV RT buffer pack (which contains DTT). So I’ve ended up with two SSII kits for the price of complaining. I guess the rep must have chased the problem up when he got back, setting a second set of wheels in motion. I’m not complaining, mind.

Oh, and apropos nothing in particular - if you’re a publisher or a journal marketroid, it takes more than one bottle of wine and three small baskets of nibbles in the foyer to get 400 scientists interested in your flagging journal. What a surprise no one stayed to talk to you.

Now I’m not saying that our labmangler is technically deficient - she’s been in the business 12 years after all - but how is it that she had trouble with BamHI and I didn’t?

I cut my vector and insert last week, set up the ligation (using minimal amounts of ligase, natch) and got a nice number of colonies on the appropriate plates. Did some minipreps, and went to the freezer to get some Bam to check for my insert. Uh . . . this looks like a new pot of enzyme. Why is there a new pot of Bam? The ‘old’ one was nearly full, and I know we don’t go through that much.

Turns out that our labmangler had trouble with Bam - if it cut at all, she was left with nucleotides. So she threw it out and got a new pot.

I can understand that; after all, it’s cheaper to get new enzyme than spend a week trying to figure out what’s wrong. But that batch had been working fine for me! I used the new pot anyway - what choice did I have? - and exactly half my minipreps had the insert I was after. So the new enzyme works, too.

I asked her this morning if the new enzyme worked for her.

“Sort of.”

Not very encouraging. What’s the difference? It’s the same buffer. Hal will laugh here, but I routinely add spermidine and BSA to my digests. Always have done, ever since I was a pup of a grad student. It saves looking up which enzymes actually require supplementing, and it doesn’t hurt, so what the heck. I’m wondering if this is real evidence that it is actually making a difference. The alternative explanation is too horrible to contemplate.

The house is so quiet tonight. Two kids devouring Harry Potter #6 after picking it up at midnight on the 16th.
Science-ah, that can wait. It is Sunday night and time for a glass of wine on the front porch. Tomorrow experiments beckon but tonight…………….. music and alcohol.

Recent SAB amusement: the posting of a list of manuscripts that referenced a truly “seminal” paper written by a certain steering committee member. Who bothers to check citations? Now we know.

FYI…you can get NEB to sell more concentrated enzymes than what’s in the catalogue. A co-worker is cloning microRNAs and needed RNA ligase at a higher concentration than what NEB sells. After calling tech support, it turns out that you can customize some of their enzymes. NEB sent the same overall units of enzyme but the enzyme was twice as concentrated. (Important for microRNA cloning because it doesn’t work so well!)
I’m not really sure how helpful this is but just wanted to pass on the info.

By the way, just heard the song…You can eat dog food by the Austin Lounge Lizards. Not something you hear everyday!

I hate spam. The electronic form screws up a brilliant form of communication for everybody, and the paper version destroys forests and bungs up the postal system.

Anachem are one of the worst offenders of the second kind of spamming. It’s probably because they’re too successful; they are the primary distributor of Gilson Pipetman®s (Pipetmen?) over here, and come on, when was the last time you bought a Gilson? If you’re really lucky and are setting up a lab, you might get to buy one or two sets (four or five in a set). But you join a new lab and you use the previous incumbent’s set, or rifle through a few drawers until you find some, get them serviced and calibrated, and you’re away. We have an excess of Gilsons in this lab. We’re saturated (what is the Km of a Gilson anyway? No, that way madness lay).

Essentially, Gilsons are too good. They don’t break. Get them serviced occasionally and they last for ever. They can be dropped, autoclaved, washed in ethanol, flamed . . . Brilliant. But there’s no built-in obsolescence so people, obviously, aren’t buying them because every month I get junk mail from Anachem with news of their latest deals on the bloody things. If there was an accident in our lab, such as - Oh, I don’t know, a nuclear meltdown and all the plastic tragically melted - and I wanted to replace my set of Pipetmen then obviously I’d know who to contact, but that doesn’t happen very often, believe it or not.

(more…)

It has been weeks since a free pizza lunch (if you get there real early and beg like a dog for mediocre cold franchise pizza). I’ve only seen a couple of sales reps in the last month and they were the good ones! Hey, I even got a freebie or two coming and I just need to cash out (you know who I’m talking about SB and TL-I’ll be calling you).
Is it just me or is the SAB site still kind of wacky? I’m getting used to repetitive posts and hitting the refresh button. But then I don’t really have too much to say. Why do people post links to Scientific American articles? I guess they don’t actually keep up with the primary literature.
Do people put SAB Perspectives on their CV? Nothing against the SAB I enjoy the fourms/debates/egos/and occasional nonsense that goes on but if I see that listed on a CV I think padding. I enjoy the forums but I’ve even seen someone (and I’m not mentioning names) listing themselves as a book reviewer for SAB. Different strokes for different folks.

Forum isn’t loading/refreshing…………………………..I wonder what I’m missing fix it, fix it, fix it!

Music: streaming www.bootliquor.com (chorus of the stream as I write this “who gives a rat’s ass baby, who gives a rat’s ass child, people that talk too much, they’re about to drive me wild”)
Food: red meat leftovers
Book: Torture the Artist by Joey Goebel
Weather: Hot
Things I hate: all terrorists

Update complaint: this blog shows the previous entry “While my guitar gently weeps….” as the most recent and this one is in the archives (okay-no great loss but……..).
Complaint still lingering: I can log on fine and then trying to update to forum “posts within the last day” the site chokes, freezes, dies and never loads. From home and work, PC and Mac. If I was a nervous guy I would wonder what I’m missing. If I was paranoid I’d say an enemy has blacklisted me. I’m neither, as I wait patiently for someone to fix the site.

I log in and see that bdoehle missed me! He truly missed me!! Tears flow down my cheeks as I realize that he likes me, he really really likes me! (Sally Fields Oscar speech reference). Okay, so there isn’t much point in posting anything. The SAB website is a mess. Posts aren’t posted or are posted in triplicate. I’m not an internet guru but somebody needs to figure this out. The site has been a disaster for a week now. It is the end of SAB as we know it and I feel fine. (REM reference). On top of that, I log on after a few days at the beach and see that Kma-haphazard is in control, broadcasting his non-scientific nonsense across the airwaves. Throw pooja1979 into the mix and you can pretty much call SAB dead until the problem is fixed. Take a vote survivor style, throw me off the island and I’ll go without a fight. I can barely read the posts. Blahhhhhhhhhhhhhhhhhhhhh.

Music: King Crimson “Discipline” (Fripp and Belew guitar combined with excellent song writing)
Food: Chicken parmigana (leave the eggplant for the freakin’ vegans)
Wine: some Aussie cab
Science meter: neutral
General mood Meter: excellent
Movie: Napoleon Dynamite (again)
Super heroine: Caped Avenger

The halls of our institution are nearly silent. Half the staff is gone, and I havn’t seen a sales rep since before the holiday. So quiet! Too quiet. hbogey and hwiegand are gone off to the beach and I’m left here with the rotation student and the Germans (nothing against them of course). New student started today. Had to explain the ordering system to her…how do you put that into words. Also cleaning up messes others have left behind etc. I could actually use a sales rep right now, break up the silence.

On another note…large scale plasmid preps are not that cheap. Anyone who has read this blog will see the great lenghts we are going through to change vendors to save a couple of bucks. So why is it that people keep coming to me as if I was a plasmid farm? I have no problem letting people from other labs have some plasmid to take off and do science with, but prep the dang thing yourself. If you don’t plan ahead and have enought for your experiment I’m sorry. I’ll try to plan better for you in the future. Ugh.

Music: Elephant, The White Stripes
Reading: Smithsonian Magazine
Mood: Missing Lab mates
Weather: 96 and hazy (that’s F not C folks)
Word of the Day: plantigrade

We had a batch of dodgy protein marker from Invitrogen. Back in January, I think it was. I made a phone call to their support desk (”We’ve not had any complaints” “You have now”) and extracted a promise of some replacement marker. Months passed, and I nearly forgot about it, until I was introduced to the new rep (I’ve talked about him previously) and in a flash of quite uncharacteristic brilliance remembered to quiz him about the replacement marker.

Turns out (after I emailed him a reminder, grr) that they’d closed the ticket because they’d sent out a replacement that, naturally, I’d never received. Got on the blower to the tech service girl, who says they have not had any complaints about the replacement batch.

“But I never received it.”

“That batch is all gone now, but there were no complaints.”

“That’s not the point . . .” after going round in circles for a bit I persuaded her to send some more (maybe it was the bit about ripping someone’s head off and pissing down the hole that convinced her) which, much to my surprise, arrived three days later, with my name on the parcel.

Score. Of course, they had the last laugh by sending two customer satisfaction survey emails out to me. I filled in one of them - and to be honest I was quite pleased with the (eventual) outcome, but I have this mental image of two tubes of Benchmark Ladder languishing somewhere in a warehouse near Milton Keynes, with no one to love them or give them a home. Poor things.

Things I must remember to blog about this month: Invitrogen versus Qiagen, Our Crazy Ordering System Part II.
Mood: Green
RiTS: They Don’t Know by Kirsty MacColl

Note added in proof:
IVGN are doing really well for themselves, aren’t they? They’ve landed the first licence in ABI’s expanded licensing system, whatever the hell that is.

The forums are useless this weekend. Postsaren’t posted, or posted twice,or maybe more….where is our webmaster? I wonder what jewels and gems were missed? A new irrational mental health theory, certainly fast breaking longevity news………….or maybe everyone took the weekend off for Canada Day, 4th of July or to just take it off…………
I’d write more but I’m afraid it would end up as the “great lost post”
Better safe than sorry……………….

I’m just wondering how long before WE get 3000 visits to this blog? Not really, I couldn’t not care less. I wonder what the percentage of scientists is who count citations/references/blog visits/etc. as a way to stroke their fragile egos? I guess it is the same ones who bitch about impact factors and the unfair nature of peer review.

Weather conditions at RDU airport: hot, steamy, humid, moist, damp, humid and steamy.

A long weekend! SAB seems to have settled down a little. Yes, our mental health expert posts incoherent conjectures now and then and our Anals of the New York Academy’s most productive author continues to plug his semi-seminal research.
I guess the sales reps were on holiday this week. Wait a minute, I did see the Qiagen rep which reminds me. I have a new mini-prep kit lined up and another kit to purify PCR products. Qiagen won’t cut us a discount and charges way too much to ship their products. Movie tickets, cheesy coolers, etc………..gives us a better price and keep the giveaways.

Does anyone remember Biowire? I still have a couple of laser pointers-they make excellent cat toys from the the go-go days of the dot.com when every company gave away something to buy a “loyal” customer base…………you still might find it floating around somewhere out there in cyberspace. What were all the brilliant MBAs thinking?

Mood-o-meter: great
Weekend plans: party/festival/cookout/parade!!!!
Music: Los Super Sever “Heard it on the X” (assorted artists-yes, the title track is the ZZ Top track)
Food: Q-Shack (Texas B-B-Q)
Movie: Mr. B’s Lost Shorts (Mystery Science Theatre)
Book: “200% of Nothing ” from the cover “An eye-opening tour through the twists and turns of math abuse and innumeracy”
by A.K. Dewdney

Please note: your comments, compliments and/or insults will not be removed from this blog. Some bloggers, well actually one old cranky blogger, gets bent out of shape and deletes comments that don’t suck up to his glob(sic).