Ode to my wife... plus a slight roast

It is my wife's birthday today. She is a magnificent 36 years young but can still act like a 12 year old when the mood suits her. She keeps me young.

I'm proud of my wife. She finished her education at 31. Not many have the gumption to stick through over a decade of education after 2 community colleges, countless withdrawals and a smattering of failed classes no less, and still she ended up at the top of her class at a UC. She's a smarty pants.

She has also stuck with me for over a decade. Do I need to explain how difficult I can be? What can I say, she must be addicted to me.

She knows how to relax. This is not a euphemism for how messy she actually is. Although, it's true that at this very moment there are at least two bras, a half dozen shirts pair of pants and several panties laying on the floor of our bathroom. No, she really does know how to turn off. I love to sit and read with her in our back yard for hours. Saturdays with my wife are heaven.

She has good taste. If you want a great recommendation for a restaurant in the East Bay, ask my wife. Our credit card can testify, she knows them all.

She is the best friend a friend can know. You don't have to take my word for it, ask anyone that knows her. She doesn't take her relationships lightly.

She's an advocate. Just ask her about beer, food, scrabble, her iphone, dog ownership, paychex, orbit gum, atheism, AAA, trying minors as adults, repressed memories, or anything else that she cares about and you'll be a convert before she finishes talking.

My wife is my best friend and I am fortunate to have met her. Please join me in saying, "Sara, thank you for being around and have a wonderful birthday weekend."

First blood

I've put a lot of sweat and tears into repairs with my motorcycle over
the years but today was the first time I had to donate some blood to
get the job done. I hope the hard work pays off and the rain stays
away when the work is done and I can enjoy some good riding this summer.

Cafe Biere

I've been super busy lately working on a paper that will (hopefully) be submitted in the next week or so. Keep yer fingers crossed. As soon as it's published I may post an update on some of the work we did. It makes a good general interest story. But, for now, it's super top secret data, so my lips are sealed.

So, in the mean time when I'm not working in the lab, I seem to find myself at or thinking about being at my new "local" watering hole, Cafe Biere. This place gets two thumbs up from me. They opened about a year ago and it seems like they're still working out kinks, like the number of taps or bottles they keep on hand (several times I've asked for a bottle that was on the menu, but not stocked), but every time I've stopped in they have at least a few great beers on tap and the food is very good. I've had a few great dishes and nothing that I didn't like. It can run a little pricey, but they have a great happy hour if you get there early, and you can't go wrong with the sweet potato fries (which come with a yummy creole aioli sauce). Give it a shot, and if you go, drop me a line so I can meet you there. It's only a few blocks from my lab... so chances are good that whenever you want to go to cafe bierre, I will be in the area. Cheers!

Working with oncogenic lentivirus

Of my few readers, I think there are only a couple scientists who occasionally visit this blog. So, I try not to talk science too much here. But, every once in a while I find something interesting that may have a broader appeal (and isn't too technical or super top secret).

I frequently read In the Pipeline, a blog by Derek Lowe. It's a good chemistry/pharma industry blog that doesn't usually get too technical. I'm no chemist but I find it pretty interesting. Anyway, from time to time he will post an entry like the one today, "Things I Won't Work With: Straight Dimethyl Zinc." To be honest, before I read it, I had no idea what a dimethyl zinc was, but it got me wondering. What biological reagents and tools are on my list of "things I won't work with?" I haven't yet come across anything that I feel all that strongly about, but I have recently pondered doing one experiment that gave me the chills.

Short background for the non-science types: An oncogene is a gene that is frequently mutated in human cancers. These genes have normal functions for most of the life of a person - usually involved with regulating cell proliferation - but at some point a cell will acquire a mutation in that gene that causes uncontrolled cell growth, which causes cancer. As a biologist I spend most of my time understanding how these oncogenes work, and hopefully - eventually - how to turn them off in a cancer cell. That brings me to lentivirus. One way we can study an oncogene is to force a cell to mutate the oncogene we are interested in. There are a few ways to do this, but the most reproducible and most "robust" method is to introduce the oncogene to a cell by way of virus. We can actually genetically engineer a virus to infect cells in a culture dish, and force the cell to express the oncogene we want to study. The good news is we can also engineer the virus not to replicate. So, we can actually control how much cancer causing virus we are working with at any given time.

Ok, enough background. This is all cool stuff but the problem with this whole scenario is that we can genetically engineer a cancer causing virus, which is capable of infecting human cells. This raises some obvious and serious health concerns. For now, I won't give much commentary, but I will say that for the time being I don't have a pressing need to do the experiment, so I have never made an oncogenic lentivirus. But I think it's worth asking before actually feeling that "need." I think I've answered the question for myself, but I was curious to hear other opinions on the topic. So, in an effort to get a little reader feedback, would this make your list of "things I will not work with?" What about others? If it were up to you, would you allow others at your institution to work with such a virus? Your direct reports? Under what circumstances would you allow it?

Tsk, Tsk, Tsk, Mr. Stewart

I think my favorite thing about the Bush years was watching The Daily Show with John Stewart. Somehow, he seemed to articulate exactly what I and most of my friends were thinking and feeling, but we never actually heard from the press. He had an ability to name exactly what was wrong with the Bush administration and at the same time he held no punches for the Democrats and their inability (or seeming lack of desire) to prevent the wars abroad or the rapid erosion of civil liberties in the US.

So, when Obama took office, I was eager to see what tact Stewart would take with new administration. What hypocrisy would he ferret out? What campaign ideals and promises would he hold the new president to? What lens would Mr. Stewart use to critique the new president of the US? Well, what is the answer? Apparently it's all roses in Daily Show Land.

It seems that Mr. Obama can do almost no wrong. It's as if Mr Stewart (along with the rest of our country) has forgotten that the US still has troops in Iraq and Afghanistan. Even when others criticize Obama for the "bailouts" Stewart is quick to point out that the bailouts were started by the previous administration, which is true... and we criticized Bush at the time. What changed? Where is the critique now? The Daily Show still makes me chuckle from time to time, but it seems like all the jokes are still focused on Fox news pundits. Yawn... that's a fairly low bar if you ask me. Actually, at this point, I tend to find Bill O'Reilly and Glenn Beck more entertaining... if you put them in the same genre as Steven Colbert. And, to be honest, Fox news has at least some good reporting happening right now (O'Reilly and Beck are neither reporting nor news).

I realize that the Daily Show has never aspired to the intellectual rigor that most good news reporting outfits do should, but at least the show was always thoughtful. Now?... well, somewhat less so. Stewart was recently discussing a new book, "Goddess of the market: Ayn Rand and the American right," with the author, Jennifer Burns. I have no idea what Burns' opinion of Rand actually is, I have yet to read the book. But Mr. Stewart certainly doesn't conceal his true feelings about Rand and free market economics. In my favorite quote of the interview Stewart said, "It's almost as if she would have a totalitarian society of individualists." I will leave you to ponder that and similar horrors such as fascist freedoms, an anarchist police state, and - my personal favorite - a regulated free market.

I never thought I'd say this, but... I miss George W Bush.

Words and phrases that make me cringe

1) Off Line - This one is usually used in a meeting at work, "maybe we should discuss this off-line." When exactly did every meeting go "on-line" and why are certain undefined subjects reserved for "off-line" discussion? I understand if a discussion strays off topic or gets too detailed for a specific audience, but can't we just talk about it later?

2) Reorientate - I know, it's actually a word, but I can't stand it. Why must we "reorientate" when we can simply "reorient?" The redundancy kills me.

3) Natural Medicine - There is nothing "natural" about medicine. That's the whole point, we take a treatment to fix a natural problem. We use reason, logic and experience to fix mother nature. Get over it.

4) Western Medicine - Do you have something against the other hemispheres? You know, Asians are perfectly capable of producing quality science (and frequently do).

5) Gourmet - This word seems like it should be reserved for something special, but if it can be used to describe a frozen dinner then I don't want anything to do with it.

6) Fascist - This is just a confusing term. I've read the entire wiki and I still have no concrete idea what the word means. I've heard it used to describe everything from totalitarian governments to a controlling spouse and even a suspect scientific finding... as in, "this experiment is so fascist." I have no idea what that means.

7) Instintaneously - This word instantly reminds me of "reorientate."

8) Their, there, they're - Just get it straight.

9) "I don't like dark beer" - The same could be said of, "I only like dark beers." I never really know how to respond to statements like this, because it's usually said out of some level if ignorance about my favorite beverage. So, consider this a teaching moment. The color of a beer has nothing to do with how thick, heavy or strong a beer is, and it doesn't even indicate how it will taste. If you don't believe me, then try a schwarzbier.

10) "If you don't vote then you forfeit your right to complain" - I think voting is fine, but complaining is just as American as voting. Besides, I have yet to find a single candidate or initiative that I feel 100% comfortable placing my support behind. Frankly, if you're not complaining, then I don't think you should be voting.

That's it for today.

That smelt's a little fishy

What was it Robert Frost said about that road making all the difference? Well, how the hell does he know?

I just read Lance's post about Sir Hannity and the delta smelt. I'm somewhat hesitant to look like I may - in any way - be perceived as a Hannity apologist, but I have to throw in my .02.

Life is full of choices. In my experience the most important choices involve some form of compromise. We usually give up something good (or potential good) in favor of something we view as better (or potentially so). I know that tearing apart Sean Hannity quotes is as easy as, well, shooting the proverbial fish in a barrel, but in the case of this smelt, what is the compromise? The topic has become a lightning rod for an old-hat debate that easily falls along the left vs right paradigm, environmentalists vs businesses, and unfortunately Hannity has become the official talking head for one side. I admit that it's difficult to separate the man from the issue, but what are we really talking about? The fate of this fish is at hand. It has been legally classified "endangered" and the experts believe that turning off the delta pumps will help. On the other side, millions of people and farms depend on the water those pumps provide. Fair trade? Well, I guess that depends if you're asking the smelt or the farmers.

John Stewart pointed out that were it not for government subsidies, these farms would not exist in the California valley. Well, that's not exactly true either, Mr. Stewart. It's true that most of the farms take some sort of Federal subsidies, but I highly doubt that some of the most fertile land in the world would be farm free were it not for the Federal government. It would certainly look different, but I doubt all farming would cease. Furthermore, is that supposed to be an argument for the government shutting off the water? If the smelt is more important than the California farming industry, then why the hell do my tax dollars go those subsidies every year? Was that money well spent?

Lastly, what assurance do we have that shutting off these pumps will save the smelt? Is it a speculation or a guarantee? If California decides that saving the smelt is a greater good than a healthy agriculture industry and the pumps stay off, will we look back and say, "that smelt made all the difference?" I wonder what the farmers will say if they relocate, leave the farming business or end up pumping water from Colorado. I wonder what the consumers will say if they pay more for their food. I wonder what the environmentalists will say, if Californian produce is once again primarily shipped from over seas.