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.

Swine Flu and The Third Reich

Since most of the hits I get on this blog are from my pharmaceutical related posts, and because I was recently given some stellar blogging fodder material on the subject, I thought I'd address the topic again. But before I do, I should point out that I am in no way a spokes person for the company I work for or for pharmaceutical companies in general, or for scientists or anyone else. I'm just a post-doc who works for a pharmaceutical company, trying to do some cancer research. Oh, and just to keep my hind parts safe I'm not going to mention the name of the company I work for anywhere in this post. Let's just call it Company X. The truth is, I could be working anywhere. The issues wouldn't change with the name of the institution.

Two Fridays ago, I was waiting outside the building where I work, waiting for my wife to pick me up, and I noticed some homeless hippie/hipster looking individuals meandering around the bus stop across the street. One was sporting some sweet tie-dye digs and he had hand-held video camera. His buddy was all decked out in black clothes, small dark sunglasses, a slick goatee and holding a stack of papers, looking like a lost beatnik. At the time I figured they were probably film students or they were on their way to an AA meeting or something, but I'll just say now that they were a little conspicuous.

Soon, Sara came by and I got in the car and as we were pulling away, the tie-died gentleman approached me and asked if I would like some information about the company I work for, "the one that makes vaccines." Sara immediately said "no thank you." But, I stopped her and said, "are you kidding? I'd love some 'information." And so, the rabbit hole of insanity began. I was given three hand-outs. One was a brochure style tri-fold that read across the front, "The [Company X] Family Tree: The Swine Flu and The Third Reich." I knew this was going to be fun. The second hand-out was a glossy 4x6 card chock-full of scary language about vaccines. Most of which, I don't even understand, but there's a picture of 3 little children crying while a blistered hand draws a syringe from a bottle labeled, "Vaccine Deaths & Autism" with a little line graph diagram skyrocketing from 1975-2009. - This is all very scientific stuff - I'm no autism and Asperger syndrome expert, but I would wager that the diagnosis of both has gone up dramatically between those dates particularly because they weren't added to the DSM until 1994. The text on the card also reads, "Just say NO to vaccines! Educate yourself before you vaccinate." Would you make up your mind people? Do you want us to educate ourselves or say no to vaccines? Which is it?

With all the craziness aside, I have to admit that the individuals were quite cordial and if I felt as strongly about a topic as they apparently do, then I would hope to go about persuading folks toward my agenda through similar means. I'm a big fan of education. It's even good to venture into the crazy once in a while, if for nothing other than to make sure you can recognize crazy when you see it. That's why I chose to respond to the third hand-out I was given. It reads exactly as follows [punctuation included, but I changed the font and various text colors just to improve the aesthetics of my blog... I do have standards]:

Questions we would like you to answer and reflect on:

So far so good. I'm assuming they want me to challenge my opinions and beliefs about the pharmaceutical industry or the use of vaccines in general. I can do that.

"what is the primary purpose of [Company X]?"

Easy enough. I think our purpose is to produce pharmaceutical therapeutics for common, unmet medical needs.

"what is your primary responsibility to; the people who buy your drugs? your share holders? the people who use your drugs?"

That's a pretty good question. To be quite honest, I'm pretty far removed from all of those people. The word, "shareholders" has never come up at work. I would say my primary responsibility is to publish oncology related research, but if I need to pick a person, I'm probably primarily responsible to the global head of oncology.

"if you found an open-license, non-patentable herb/substance/chemical that would 100% cure cancer, would you market and sell it?"

Ok, we're getting to the good stuff here. I think this touches on a few misconceptions about the pharmaceutical industry, but first I'll answer the question as best I can. I have nothing to do with marketing, so I can't really answer it directly. But, you bet your ass I would characterize, publish and be a huge advocate for any herb/substance/chemical, compound, treatment, therapy or rain dance that 100% cured anything, and particularly if it cured a cancer.

Now, the scientist in me has to point out a few things. First, there is no secret cure hiding behind the walls of big pharmaceutical companies. If I knew of a cure, I would publish it even if I couldn't make any money on it, just because I'm an ego-maniac. I would want everyone to know that I found the cure for cancer. All of the scientists I know are the same way. Then, after I published it, I would still manufacture and sell it. Who would you want to buy your "cancer cure" from? I'll buy mine from the guy who discovered it. You don't need a patent to make money from selling a drug. Did you know that Bayer's patent for aspirin expired almost a hundred years ago? Isn't it crazy that they can still sell boat loads of the stuff?

I will leave the complications of discovering a "cure" for the next question.

"would you market and sell a drug that would cure cancer at any level (not mediate but cure)?"

Yes.
Okay, now that my answer is out there, what do we mean by "cure?" because if you mean symptom free survival, then we already have "cures" for some cancers (although I agree, not nearly enough of them). And if you mean that it increases survival rates, then we have many more "cures." But, if you mean that 100% of the cancer is removed from the patient's body, then the issue gets muddled a bit. The semantical problem is that there's always a chance that cancer can come back. It's always possible that a single cancer cell is still hanging around and will start growing and make a new tumor at some point. That's why we call it "remission." So, even if we found a "cure" that was, for all practical purposes, 100% effective, unless you surveyed every cell in a person's body to prove no more cancer survived, we would still call it remission. Even then, I'm sure the lawyers would insist that no one ever mentioned the "C" word.

"Do any of your drugs actually work to cure, or fix problems, or just mediate or slow down a problem?"

Company X drugs? Yes. Specifically, I know of several. I only know of one in oncology (imatinib used for CML), but there are more in other disease areas (one of them is actually given to third world countries for free, and as a result leprosy is now basically eradicated). To answer the subtext of the question, no scientist I have ever met has ever intentionally produced a sub-optimal treatment for cancer. The goal is always to produce the most effective treatment possible. The goal is always to cure. The shitty reality is that cancer is an outstandingly complicated disease and, so far, we seldom do better than to extend the life of patients by a few months or years. But, I'll keep working on it and so will thousands of others.

"Since people take your drugs to fix problems, where are the now healthy people that are not taking your drugs any more" Any at all? why?"

Well, I met 3 of them last year. It was fantastic to hear from patients that had taken one of the drugs produced by Company X and are now in remission. But, personally, my mother had Hodgkin's lymphoma, which is a very treatable cancer. She is also now in remission and no longer takes any medications. But, it was several months of intense radiation and chemo, followed by a few years of post-treatment. Thank the gods there are people out there who took the time to find a treatment for that disease and good-on-em if they made money doing it. I'm sure they deserve it.

"how much money does your company need from the government to make a profit?"

Good question. I'm sure the answer is none. The pharmaceutical industry is the most lucrative business out there. That is not to say that pharmaceutical companies don't take any money from governments. I'm sure they take a lot, but they don't need it, and I would be 100% in favor to stop tax dollars from going to any company, pharma included.

"Can your drugs be used along-side homeopathic remedies and natural medicine? Why? Why Not?"

I suppose it depends on the homeopathic remedy. But, I would wager that the answer is usually yes, take your echinacea along with your cancer drugs. It probably won't hurt. It won't help either, but it won't hurt. I was always under the impression that most "homeopathic remedies" won't work unless the patient stops taking "traditional medicine." I've never heard of a cancer drug losing efficacy if taken alongside oleander soup.

So, there you have it, straight from a post-doc working for big pharma... for whatever that's worth. But don't take my word for it. Do your own reading and make up your mind for yourself. It won't take long to recognize the quackery where it exists. Thanks for the dialogue and keep the questions coming.

Frodo Good, Harry Potter Bad

I used to listen religiously to the focus on the family broadcast... not because I agreed with them, but because I could recognize their massive influence on how many Christians in the US view the world and think about contemporary issues. I also used to write them on a somewhat regular basis... I know, what a dorky waste of time. It's true. But, I do think there is some educational and entertainment value there.


Anyway, the recent Harry Potter film reminded me of one exchange. I asked simply, "Why is Harry Potter bad and Frodo Baggins good?" This was their response:

Greetings from Focus on the Family and thank you for your e-mail to our ministry headquarters. I consider it a privilege to reply on behalf of our staff.



Thank you for your recent e-mail regarding our perspective on Harry Potter versus Frodo Baggins. Having evaluated each of the _Harry Potter_ books in the series, our staff has found there are aspects that may give Christian parents reason to pause. Magical characters -- witches, wizards, ghosts, goblins, werewolves, poltergeists, and so on -- fill the pages. While the author certainly distinguishes “good magic” from “bad magic,” it’s difficult to ignore the trend toward witchcraft and New Age ideology in the larger culture and not consider the effect these stories (albeit imaginary) might have on young, impressionable minds.



From a broader perspective, we believe it is important for parents to pay close attention to the manner in which spiritual power is presented in *any* story -- not just the _Harry Potter_ books. It’s crucial to ask questions like, “Who is the source of this power? How is it portrayed? What are the results of its use?” Good spiritual power -- for example, the power by which the apostles healed the sick and the lame in Jesus’ name -- comes from God. He gives it to His people to accomplish His purposes, and it is always used for *His* glory. Occultic or evil spiritual power, on the other hand, serves the user’s own selfish interests. It is dangerous, destructive, and manipulative in nature.



As a sidelight, it’s worth mentioning that there are many cases in which the powers exercised by fantasy and fairy tale characters have no spiritual significance whatsoever. Such “magic” is simply a part of the make-believe world created by the storyteller -- a world which operates according to principles of its own and suspends the rules of normal day-to-day reality. Even books written by Christian authors from a Christian perspective -- for example, C. S. Lewis’s _The Chronicles of Narnia_, J. R. R. Tolkien’s _The Lord of the Rings_, and the fairy stories of George MacDonald -- make use of this device. The ability of Cinderella’s fairy-godmother to turn pumpkins into coaches, Mary Poppins’ talent for sliding *up* the banister, Peter Pan’s aeronautical skills, and Alice’s wild experiences with shape-altering mushrooms all belong to this category. Here again, parents must use discernment in determining which stories fit this description and which can be justly characterized as occultic in nature and intent.



With these thoughts in mind, we’d like to suggest the following rule of thumb for evaluating fairy tales, fantasies, and fictional stories of any kind. Any story that exhibits a tendency to romanticize the occult should probably be avoided. If, on the other hand, a work of fiction portrays the practice of witchcraft and wizardry in such a way as to highlight its evil nature and make it unattractive to the reader (as in the case of C. S. Lewis’s White Witch), then it is probably acceptable from a Christian point of view.



Thanks again for seeking our thoughts on this matter. We hope this response has been helpful. May God grant you wisdom and direction in the days ahead.


Ken Wolfe
Focus on the Family

Is that clear? Anything C. S. Lewis and Tolkein write is good because their magic is imaginary. Whereas the magic Harry Potter uses is real... and Harry Potter is a selfish occultist wizard, and that's bad. Got it? Still I do give them credit for advising parents to make their own judgments on the issues. Isn't that really the only answer? Of course, that should beg the question as to why they endorse one but condemn the other, but who's keeping track?... people like me.