Monday, February 25, 2013


Justus Von Liebig statue in the snow in front of the school named after him, in Darmstadt, Hesse, Deutschland.

Saturday, October 13, 2012

An atheist moves to the south...

I was raised in southern California. Due to the mortgage meltdown and instability of working in drug discovery I moved with my wife and daughter to St. Louis, where I have family. I didn't manage to find anything permanent there, but took a job in Columbia, MO working for someone that would be a better used car salesman than owner of a sample prep instrument company.

Now I am back to working with LC/MS systems... or rather I should say working on them. I am now an LC/MS field service engineer.

To get the job, I needed to relocate to Memphis, TN. After a period of training in St. Louis with other FSEs, I have just done so. Today makes just over two weeks living in the south.

We found a nice house to rent in a quiet, safe neighborhood. There are a good number of kids on the street for my daughter to play with. So far so good... but people seem bent on knowing where you go to church. I have so far dodged the question, but they are catching on. Also, my daughter basically told another kid that we don't go to church. Her mother asked my wife yesterday if we "worship God." My wife is on the fence on the question of existence, and I think slowly moving away from belief, I am not pushing her. I have considered myself an atheist for almost twenty years now.

My main concern at this point is that the other parents on the street will ban their children from playing with my daughter which would be very painful and hard for her to understand at only six years old.

I just really wish I could fly below the radar here for a bit longer, but it doesn't look like it's going to be possible.

Thursday, June 14, 2012

An adventure with VBA for Excel and LC/MS

I have routinely used Visual Basic in excel to help automate sample list creation and data handling for LC/MS on various platforms. This was terribly helpful when I was running ADME assays since I was able to come up with several plate formats which varied by assay and simply plug in the compound IDs and molecular weights. Generally it was possible to simply make templates in Excel, and export a sheet as a CSV file which would then be imported into the LC/MS software.

But then came the Varian 5oo MS.

It wasn't a bad mass spec, but it had a horrible sample list editor which would absolutely not let you import a sample list. They also had nerfed the ability to meaningfully paste within the list editor. I could only copy and paste whole lines, which meant I couldn't just copy and paste one field into a whole column. I was truly disgusted with the lack of usefulness of this. I also found that very few people believed me when I said I couldn't import or paste a spreadsheet in this program. Nobody was able to prove me wrong though.

 Since I was typically trying to run between one to four 96 well plates of samples at a time, it could take well over an hour to manually create a sample list. To make matters worse, I didn't have the autosampler I wanted which would have been a CTC PAL. I had an autosampler that would only hold one plate. On the upside, it could be a 96 or 384 well plate, and we had a Janus robot that could quickly make one 384 well plate out of 4 96 well plates. The downside of the upside is that the samples were then laid out in quadrants, so well A1 was from plate 1 well A1, well A2 was from plate 2 well A1, well B1 was from plate 3 well A1, and well B2 was from plate 4 well A1, and so on.

I wanted to run each of my original plates in order but because my samples were laid out in quadrants it became a dreadful and error prone task to fill in the sample list manually. Again, if the software would have simply allowed me to import an Excel or CSV file I could have simply thrown some templates together and gone on with it.

What I did was to get curious. What is the data structure of the sample list file that the software creates? Can I see inside it and make sense of it? The first attempt is always just opening it as a text file, but that is rarely useful, so I hopped on the internet and learned about hex viewers and reverse engineering file formats. Using a hex viewer allows you to see the actual bytes of data in a file and the one I used allowed you to interpret that data in various ways. It also let you compare two files for differences, and this was the key.

I started by making short simple sample list files that differed in only one way at a time such as: well location, LC/MS method, compound ID, molecular weight, or the comment field that I found crucial for tracking assay conditions for that well like time for a stability assay or concentration for an inhibition assay.

I was gradually able to tease apart what format numbers were written in, how large the text fields I used could be and if they were a fixed size, and pretty much any field that I bothered to fill out. I was still left with large parts of the file format that were unknown to me, but what I did was to steal valid strings from a file created by the native software and just paste them in as needed.

In the end I had a spreadsheet macro that could write the exact same file format as the LC/MS software, at least as far as I needed. This let me take a bunch of excel templates for various assays and drop in minimal amounts of data to create sample lists with no chance of transposing well locations (in the spreadsheet anyway), running the wrong method for the wrong compound (unless the error was at the bench), and it wouldn't take a huge chunk of my afternoon, which allowed me to focus more on the performance of the assays and ensuring the LC/MS system was running properly.

Since then Varian was bought by Agilent mostly for their NMR line, and I presume that the Varian 500 MS is only a brief blip in the mass spec world. However, if anyone is struggling along with one, I do still have that Excel macro.

Wednesday, March 14, 2012

Euphemisms for being laid off.

Back about seven or so years ago, Pfizer decided that it had too many people engaged in drug discovery (again, and certainly not for the last time.) This came on the heels of purchasing Pharmacia, another sizable company, among others acquisitions.

So meetings were called, not that that was unusual. The masses were informed that "We're too big now. We need to find some way of dealing with how gosh darn big we are. We need to start 'Adapting To (the) Scale' of how frigging big we have become."

Thus the "Adapting to Scale" or ATS initiative was born.

Of course the best way, they said, to adapt to how big you have become is not to adapt to it at all. The best way is to become smaller. And we are busy figuring out where we are too big. We will let you know in about 3 months where cuts will be made.

Three months.

It's very hard to focus on your work for three months while the sword of Damocles dangles above you by an increasingly weaker looking thread.

Three months came and went. So did four and five. Around the six month mark, the rented circus tents were erected, site meetings were called, and announcements were made, but only the most vague. The real information trickled down the hierarchy over several days or more.

Slowly, we learned who was being "ATSed". The uncertainty over all that time had eroded the morale of many, including myself.

It is cruel and unusual (is it unusual?) punishment to leave thousands of people in the dark for so long after letting them know that there is to be a cull. It is even more cruel to try to put a happy face sticker on out and rebrand it as a positive thing.

That Pfizer had problems to face was no secret. That R&D was big and not very effective was also well understood in the trenches. What was shocking was the callous disregard for a well educated workforce. How could they think that smiling while they brandished the knife for so long would ease the pain?

I was not "ATSed" or "Pfired", as people started calling it. The damage was done though. I moved on not too long afterwards, which I will never regret, even though that later company went under in a few years.

Drug discovery, it seems, can be a meat grinder. I had survived two rounds of cuts, but for what? The collateral damage spread out. Other pharma companies followed Pfizer's lead and cut back significantly. To this day the industry is still hemorrhaging jobs.

Now I am trying to find my footing on a different path.

Wednesday, February 29, 2012

The carrot or the stick.

Some managers believe they can motivate their employees with the "carrot", and that the carrot can be many things in addition to monetary compensation. I fully agree with this viewpoint.

There are other managers that feel that they can motivate their employees with the "stick." They believe that they can keep people moving forward with the threat of negative consequences. I feel that this style of management has been shown to be ineffective again and again... unless the effect you want has little to do with productivity and more to do with fulfilling a sadistic manager's impulses.

I have a manager who believes in the worst possible combination of both ways. The threat of the stick is there, but he knows not to push his more educated employees too far, even in this economy. So instead he puts the carrot at the end of the stick. It's the reward that will never come, but at least I have realized what my situation is.

Nobody should ever have to feel threatened in order to do their job. Nobody who feels threatened will ever be capable of doing their best job.

For anyone in my position there is only one solution: move on.

In the meantime, I will document my experiences, anonymously, as I will be saying all the things you are not supposed to be saying about your employer while job hunting.

Monday, February 27, 2012

Title below.


The story so far: I had a career, but that seems to be on hold. In place of my career, I have a job. My job had the potential to be a good career move, but any resemblance between the two is not even coincidence, it's an hallucination.

I have had some really good positions in pharma research, but it has been quite a bumpy ride, which if you know pharma is not surprising. I have had two companies sell off or shut down operations in my area. I survived several rounds of layoffs at a big pharma company only to leave in disgust. I also moved on from a few other positions for other reasons. I generally like what I have done at all these places, which has mostly been to provide analytical chemistry support for medicinal chemistry groups. I don't want to get too specific, that's what LinkedIn is for. What LinkedIn is not for is rants about shitty jobs, that is what blogs are for, or at least that's one application anyway.

So I thought working for a small analytical instrument manufacturer might not be that bad. Well, it could be not that bad. In fact, it really does have quite the potential to be an enjoyable and rewarding job. It could even pay halfway decent, at least for the region, which is to say the middle of nowhere, but it doesn't do any of those things. It's miserable. Why? The owners. They simply have no business at all running this sort of company. I don't know all the details of how they came to be in this business, but I do know it has been a series of unfortunate events, at least for their employees. What is the name of this company? How do you avoid working for them? That is not what this blog is for. That is what is for. It is also what was for before it got neutered and renamed.

So what's wrong with my job? Tune in next time... and probably the time after, and the next one too... For now let's just stick with "I'm underemployed."