Life Science Tools of the Trade

I hate phones. I don’t have a cell phone. I let the answering machine pick up 99% of calls at home. At work I answer the phone. Not because I’m looking for another annoying cold call from Dipshit Biotech but because I have a wife and two kids there are times I need to be reached. Plans change, illness, car problems, etc. So……….

Today the phone rings in the lab. I’m in the middle of setting up a fairly complicated experiment. “Hi Hal, I’m ____________, you probably don’t remember me but you sent me some reagents several years ago and I want to do another experiment and wonder blah blah freaking blah.”  Short of hanging up (why didn’t I think of that), how the hell can I escape? Ten minutes later I’m back at the bench, dazed and confused. Did I finish the master mix. Start over…………..not enough left of one reagent………..I find more but it is another prep…recalulculation time……….feelings of failure…finally I toss the whole thing in the trash can……….”That bitch”….ooops, that costs me a quarter to the lab curse jar.

But it was worth it. Money well spent.

Tomorrow?

 ”One more chance to get it all wrong”

(lyrics courtesy of the Replacements)

I apologize for my lack of writing the last month. April passed by in a blur for me with final touches and preparations for my wedding followed by two weeks in Italy on a honeymoon. Needless to say that’s ALL that I accomplished for the month. BUT what an accomplishment!!

The wedding was great! We celebrated with family and friends and were married at the end of the day. The following day we were off to Italy - a first time visit for both of us. A few days in Venice, a few days in Florence, and to finish off the trip a few days in Rome. Not a lot of science. Actually there wasn’t any science but there was a lot of history, art, good food and good wine.

A wonderfully memorable and exhausting trip!!

In this post-90’s biotech era which we all inhabit, I’m finding that brand recognition is becoming a confusing game indeed. Old favourite boutique vendors like Molecular Probes have been swallowed up by enormous, multi-tentacled distributors like Invitrogen, and keeping track of who’s distributing your favourite brand of pipettor, or water filter, or tissue culture media, can make for hours of fun and games. Even the big players keep getting bought and sold – just try to sort out the whole Merck/EMD fine chemical business, or the ownership structure of VWR, if you have some time to kill. And I’m still trying to get my head around Thermo Fisher. What does Thermo Electron have to do with distributing pipette tips and latex gloves? How, if at all, is this related to Thermo Finnigan? It makes my head hurt just thinking about it.

And then there’s my personal favourite suite of technologies du jour, loosely grouped into “next-generation” DNA sequencing, or NGS. Illumina buys Solexa, Applied Biosystems buys Agencourt Personal Genomics (but not Agenourt Bioscience, which is owned by Beckman Coulter – are you following this?), Roche gobbles up 454 Life Sciences. Pacific Biosciences is next, mark my words, with rumours of intense interest from Applied Biosystems, and probably many others. Helicos too, perhaps, so look for a merger or acquisition there, although with a market cap of $147 million and $50 million in the bank at the end of 2007, they could probably stay on their own for a while.

In the case of Illumina’s almost-works-most-of-the-time Genome Analyzer, most people still call it a “Solexa”. At the recent AGBT conference, which I’ve rattled on about in more detail elsewhere, practically the only people using the term “Illumina Genome Analyzer” were members of the large posse of Illumina employees in attendance. And most people don’t call the ex-454 machine a “Roche” GS-FLX; to most, it’s still a “454”, although this seems to me to be waning a bit under the crushing weight of Roche’s marketing machinery. Remarkably, the 454 Life Sciences website still exists, and is still a much, much better source of information on this NGS system than the Roche website, which is large, messy, and rather full of the 150,000 other things that Roche sells.

On the other hand, Applied Biosystems seems to have triumphed in branding their SOLiD system, and virtually nobody seems to remember that this was developed by Agencourt Personal Genomics and that the chemistry used was, for a time, referred to as the “APG process”, even by AB itself. Now it’s just SOLiD, small “i” and all, and the scientific community in general seems to have accepted that brand. Timing, I suppose, is everything.

Now, if someone could just explain to me why all these darn NGS boxes are blue…

Well, as Kat mentioned over at the SAB, I am now activated, Word-Press-enabled, and ready to jump into this whole Life Science Tools of the Trade thing, joining my virtual colleagues hbogerd and hwiegand.

As some of you know, I’m a Blogger kind of person so far, so this post is as much about introducing myself as it is about seeing whether I can work out how WordPress works. So far, so good, nothing’s caught fire yet. I will doubtless be posting many erudite comments on the technologies we all use (or more likely, those that fail us miserably), but in the meantime I’l leave you with a teaser: yes, we have a next-generation DNA sequencer; no, it doesn’t work as well as advertised; and we just finished our first client project, a ChIP-sequencing experiment, after seven months of trouble-shooting since delivery. That’s about average, folks.

At a vendor fair I picked up a free sample of Agarose Tablets from BIOLINE! The little white pills of agarose eliminate the  messy task of weighing out agarose! Okay, unlike LB powder or SDS, weighing out agarose isn’t really that messy. The little pills do save you the time you’d spend weighing out the agarose. Unfortunately, the pills have to dissolve for for 6 minutes in your buffer before you can microwave/melt them. Okay, no time saved. Safer to use?? I have no idea what that even means. The agarose tablets are probably MORE dangerous. Swallow one of those suckers by accident and I bet you’d be plugged up for days. Oh yeah, and they’re more expensive.

Thanks but no thanks.

The full text article is available for purchase

$59.66 plus tax

for a  1991 Virology  article? 

No thanks. I wonder what is the highest price a journal charges for access to an article? Does anyone actually buy single articles? More importantly, why am I trying to get access to that crappy (probably)  old (definitely) article on Sunday night?

Bill Clinton’s memorable attempt at legalese evasion (what the definition of “is” is) during the Monica Blewinksy hearings made me wonder what the dfinition of “it” is. Today I wore my Promega promo t-shirt. The slogan? “Research makes me do it”. It? It depends on what your definition of “It” is. What does research make you do? It certainly doesn’t make me do “it”.

Has the High School musical craze reached the science world? If you haven’t seen Bio-Rads PCR song, you need to check it out!

Scientists for better PCR

I’m still undecided. Is this suppose to be taken seriously?

I received a flyer for Clontech’s In-Fusion PCR Cloning System in the mail. I do try and scan the junk mail I receive, looking for the jewel in the junk. In-Fusion is a method of cloning that uses regions of engineered homology on your PCR generated insert and vector of choice to ligate without cutting your PCR fragment. Interesting. Maybe. Looking at the “time saved” flow chart. 30 minute ligation insead of 16 hours! That saves an entire day….if you still ligate overnight. In fairness, a footnote (in small print) reads “newer 5 min T4 DNA ligase reactions could be used”.   The real laugher is provided by the jokers in advertising when they comapare In-Fusion’s cloning efficiency with T4 DNA ligase’s. In-Fusion, obviously, is rated “High” (surprise) for both  .1 to 4 kb and 4 kb to 10 kb inserts. T4 DNA ligase PCR Cloning? No data available! Really? No data available? In-Fusion is better, much better when we compare it to “No data available”.

Clontech looks like a contender for the BioTech Bullshitter award for 2008!

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The Magic Eight Ball says “Doubtful”.

I complained about the ridiculous and useless plastic boxes Operon started sending out if you ordered a single oligo in this blog a month ago. I received two shipments of oligos on Friday (1/11/08) in the paper sleeves of old. Did Operon listen or did they just run out of the Operozone destroying boxes?  I’d like to think they listened to a wave of consumer complaints. The next couple oligo shipments will tell.

Having ragged on Operon for their environmental blunder, I’ll add that Operon oligos are great quality at a great price. I  wonder if the bozo (with the MBA) that came up with the petroleum product oligo carrier was fired?

sure makes it hard to get much stuff accomplished on the Monday.  Set a few things up.  In general, though, I didn’t want to set things up that I’d have to worry about tomorrow.  Thanks to my cells looking weird this morning I’ll be in briefly to do a transfection.   Other than that it’ll be a quiet, relaxing 1st of the year.

Have a great start to the New Year!

For many months I’ve been getting science equipment fliers/magazines sent to my home address.  Somehow my name got sold and I’ve been getting all kinds of crap - AT HOME!!  The worst part is trying to gett them to stop sending stuff.

One *subscription* was finally expiring.  At least that’s what the telemarketer kept saying when he called the lab daily.  I think, finally, they got the point.  Sorry to Hal and the others who kept fielding these annoying calls.

To all you companies:  Please don’t call anymore, take me off your list, I don’t want your magazine(s)!!

Please.  Save a few trees instead.

Are you listening?

Plastics.

I guess someone at Operon saw “The Graduate” and took that advice to heart. I used to receive oligos from Operon in a paper corrugated sleeve. It could hold up to eight oligos. You could reuse it, recycle it or just throw it out and not feel too guilty.

Today I received an (meaning literally ONE) oligo I had ordered. It came in a plastic box, clearly marked OPERON, with a difficult to remove recessed lid as an added bonus. It must use about 20 times the plastic that was used in the screw top oligo tube.  I guess you could use it as a semi-waterproof bullet box on weekend deer hunting trips.

As most manufacturers (and consumers) make an effort to use less plastic in their packaging I’d like to nominate Operon for the “We support global warming award of 2007″!

Posted on Thursday, December 13th, 2007 at 11:43 pm You can follow any responses to this entry through the RSS 2.0 feed.