New post over at Scientopia!

Hey, I wrote a new post over at Scientopia about how to run a lab when you’re not there. Go check it out and update your feed readers and bookmarks to my new site!

It’s moving day!

So, readers, I’m happy to announce that I was invited to blog at Scientopia. So I will be moving “Take it to the Bridge” over there where you will find all my old posts and comments and all of my new material. This site will remain, up but not updated.

So update your links and feed readers to my new home: http://scientopia.org/blogs/bridgeblog/ and see you over there…

Commander, set course for Scientopia, warp one… Engage!!

Open lab 2010!

Not to brag or anything, but one of my posts “Neuronistas vs. Reticularistas” was selected to show up in Open Lab 2010. This means that it will appear in this years anthology of the best science blog posts of the year! Thanks to the editors for selecting my contribution!

Paella!

Oh no! The holidays are over and you intended to have your colleagues over to your house for a little holiday celebration. Nothing big, just your favorite faculty colleagues, maybe your department chair, bring the family, have some spiced cookies and nice wines, a little rum. But you fucked it up, the holidays came and went and you missed your opportunity to socialize and show off your hosting skills. How can you have them over now? Everyone is on holiday withdrawal, plus spiced cookies sound so 2010.

But there is still hope. That’s right, invite them over for paella! There’s nothing to cure a depressing winter sunday afternoon than a leisurely lunch of steaming, fragrant paella. A veritable treasure chest of delicious goodies that will not only showcase your cooking skills but will show off your international sophistication and élan.

So how do you make said paella? In Spain, they typically make paella with either “land” meat (rabbit, chicken) or with seafood, but not usually with both. It is typically cooked over a wood fire and requires patience and artistry passed down through generations. Down in Mexico, we disregard these silly conventions and mix everything together. This recipe uses a mix of seafood with sausage and chicken, but feel free to use any combination of meats and seafood. While the recipe may look daunting, it is actually very easy to do. If you want a test run, you can limit the types of meat used, or even try a vegetarian version (but this is not recommended – I think rabbit will impress your colleagues more).

You will need:

Olive oil

6 chicken thighs

4 sausages (chorizo, sweet Italian, whatever)

Shellfish (mussels, clams, etc. – calculate about 4-5 per person)

Un-peeled shrimp, or large crayfish (2-3 per person)

Squid (hoods and tentacles -1 squid per 2 people)

1 onion, quartered

1 red pepper cut into strips

1 cup frozen or fresh peas

About 4 cups of rice (see below)

Chicken broth (or water)

Salt and pepper

2 bay leaves

2 hefty pinches of saffron (or substitute 1/4 tsp of turmeric, but saffron is way better)

In the largest skillet you own, first brown the chicken and whole sausages in olive oil, sprinkle some salt and pepper on the chicken, and cook until the chicken is well browned and the sausages are cooked. Remove the meat and cut the sausages into thirds. Next briefly saute the red pepper and remove from pan. Briefly saute the quartered onion and then start adding the rice. The rice should cover the bottom of the skillet and should be no more than half an inch high. If your skillet is too small, use two skillets. Once you add the rice cook the rice in the oil for 2 minutes or so until it is nicely coated and shiny. Gradually add the broth until it covers the rice, about 1/2 to 2/3 inch above the top surface of the rice. Add the saffron and bay leaves, stir and bring to a boil. Once boiling, stir once more and lower the heat and arrange the chicken, sausage, red pepper strips and peas over the rice in a single layer. Cover the pot, raise the heat for a minute or two and then lower heat. Wait 15 minutes (go make some sangria or something). After 15 minutes take a peek. The rice should be mostly cooked. If the liquid level is too low and the rice is very undercooked add very small amounts of broth to moisten, but not submerge the rice and cover and cook for a bit more. When the rice is almost done, arrange the seafood on top, again in a single layer. Add maybe a little more broth (about half cup, unless it is still soupy, then don’t add more) to generate some steam. Cover, raise heat until you hear boiling noises and lower. Check every 5 minutes or so until the seafood is cooked (ie. shellfish has opened, shrimp is bright pink and squid is “curly” but not rubbery). Bring the whole pan to the table, call your colleagues and enjoy! Serve with plenty of sangria…

Sometimes, reason does prevail

So in what now seems like a different lifetime, I had written about an issue we had had with The Third Reviewer and one of our manuscripts at a Fancy Journal. To summarize, we had two initial good reviews who had agreed to accept the paper, when the journal decided to add a third, who trashed the paper and thus, this being a Fancy Journal, got the whole thing rejected. Against all odds, we went on the warpath against this reviewer and appealed the decision, this never having worked in the past.

And… ten weeks later WE WON!! Paper is accepted, Third Reviewer has been vanquished, and a piece of the Mojo Banjo has been recovered! Now it’s time to…

Patience, young Grasshopper…

“How are you feeling this morning Mr. Namnezia?”

“That’s fucking Dr. Namnezia to you, you little intern. And I would be feeling better if you hadn’t fucking burst into my room without knocking and turned on the light and scared the shit out of me.”

“Oh, sorry about that Mr. Namnezia. Are you in any pain this morning?”

“Look you little fuck with your little suit and tie, none of the other interns wear suits, they wear scrubs, and at least express some sort of sign of humanity when dealing with patients. Why are you wearing a suit? You remind me of all those over eager premeds I teach everyday. Maybe you can spend some time developing some real bedside manner rather than the fake concern and “professionalism” you are expressing now.”

“Are your bowel movements OK?”

“Fuck you!”

And the worst thing about all of this, is that despite me wanting to say all this, I didn’t. I just answered his questions obediently, let him listen to my insides and let him off, with his smug sense of authority. This is one of the hardest things I’ve had to deal with in being a patient, basically becoming an object, a body to be treated and not a person. Having spent last week in the hospital (I’m home now) really took a lot out of me, both physically and mentally. After a week of not walking or eating much I am ridiculously skinny/weak and my body does not feel like mine. During my stay I was visited by a slew of hospital doctors, and every time I would have to explain my whole situation as they poked and prodded me during every shift change. Plus of course nurses coming in  and out to give you medication, silence your beeping I/V pump, take your vitals, draw blood, etc. And in all of this the stress of making sure things stayed clean and that nobody made any mistakes. The whole thing is very dehumanizing. Not just being in the hospital, but being a patient in general.

In the 1960′s French philosopher Michel Foucault wrote in “The Birth of the Clinic” about the emergence of the “medical gaze” in the medical profession since the late 18th century. The idea being that a doctor cannot look at a patient as a whole person, but rather as a body, with a bunch of symptoms. Now, I have to admit that the only reason I’ve read Foucault is due to my undergraduate institution’s penchant for adding obscure poststructuralist philosophy to pretty much any class. I also have to admit that I can only can makes sense of about half of a things Foucault says. But after being in the hospital, his point becomes incredibly clear. It is a dehumanizing experience.

So what is there to do? Ever since I got sick I’ve been approached with offers of complementary medicine – Reiki and such. They say these are for the mind, conventional medicine is for the body. But why? Why do I need someone reorganizing some energy forces or whatever to make me feel more human? Why can’t regular medicine be for both? Why can’t it be more human? And I really think that the solution is simple – it’s called good bedside manner, listening to patients and treating them well and like equals. That’s it. But I found this lacking in so many doctors.

That’s not to say all doctors are like this. We were fortunate enough to find a doctor who really takes his time to answer all of our questions (between my wife, brother and I being scientists, believe me, we’ve put him through the ringer) thoroughly and intelligently, has been great at helping us get second and even third opinions, facilitating medical literature and just overall caring. He welcomes emails with questions and checks in at random times to see how I’m doing. Likewise, in the hospital there were a handful of nurses that you could tell went above and beyond to provide good care and look after your best interests. So medicine need not be so dehumanizing, it just takes someone to care and listen to make a huge difference.

One thing I’ve learned about this is that in order to make my body mine again, I’m going to have to put up with being poked and prodded for a while, but hopefully, little by little I can reclaim myself again. That slowly I will fatten back up and regain my strength and feel like me again. But for now the most important thing is to maintain perseverance, strength and most importantly patience. And to stay out of fucking New Jersey…

I’m just mad about saffron

Note from Namnezia: The following is a guest post from my smart and lovely Supercool wife, who has been indispensable in navigating this bumpy road. Enjoy!

Having only been in the hospital for the birth of our children, I guess I didn’t know what to expect when we showed up in the hospital 3 weeks ago and were given what can only be described as a knock-out punch to the stomach.  In the past three weeks, we have dealt with pneumonia, lymphoma and some serious hemolytic anemia that has us talking about types of red wine every time my husband visits the loo.

Being a scientist myself, maybe I expected nurses to hand us daily charts and graphs, detailing progress.  I expected protocols and treatment plans that wouldn’t change hourly.  During the day we spend so much time focusing on the science of what is happening – a crash course in cancer biology, hematology and immunology.  At night when I lie down to sleep in a cot placed too far from my husband’s side to actually reach him, I listen to the monitors beep throughout the oncology ward and I wonder how did my love become part of this cruel experiment with an n=1?

Aside from his physical appearance my husband remains unchanged.   Thankfully, his sense of humor is safe from the cancer that has invaded his body.   Immediately following his first round of chemo, to which he responded with rigors so severe it was as if he was undergoing an exorcism, he opened one eye and with the little strength he had left, said to the oncologist, “That is some wild shit.”

His jokes have taken on a bit of morbidity but he throws them around with the same spirit as always.  When the bad news started coming in, he didn’t want to hear it all at once and let the oncologists know by telling the following joke.

“So, a man is going on vacation and asks his neighbor to look after his cat for the week, and to call if anything was wrong.  On the first day of vacation, the phone rings.   The neighbor says, “I’m sorry, man, but your cat is dead.”  The man is distraught, cannot enjoy his vacation and promptly returns home.  He says to his neighbor, “Listen, you ruined my vacation.  If you have bad news for me, you should break it to me gently.    You could have called on the first day and said, “Hey, your cat is up on the roof.”  On the second day, you call and say, “Hmmm….your cat is close to the edge.”  On the third day you call and say “I’m really sorry, but your cat fell and might have broken a leg.”  Fourth day, “Man, your cat isn’t doing too well, he might be a coma.”  Fifth day, “Sorry, but your cat is on life support.”  Sixth day, “Maybe you should come home.”  Seventh day, “Sorry, but your cat is dead.”    The neighbor apologizes.  Next year comes around and the man goes on vacation again, instructing his neighbor to call if anything goes wrong.  On the first day of vacation, the phone rings.  It’s the neighbor and he says, “Man, your grandmother is up on the roof.”   My husband is not on the roof, but these past few weeks have definitely been an uphill climb – with bumps in the road as big as mountains.

Now – to get to the title of this post.  I’ve always been pretty ambivalent about the color yellow.  Didn’t really love it – but really had nothing against it.  Well, now that’s a different story.  Yellow can instill panic in me – but can also instill a sense of calm.  It is all about placement.  Yellow – and all colors for that matter – should stay where they belong.  Yellow should not suddenly show up uninvited in the skin, but should be a color that one sees when visiting the commode.  Quite rightly, mustard nitrogen – one of the chemotherapy agents – should not be going into my husband’s body.   I’ve been thinking a lot about yellow recently, and can definitely say that I am a bit mad about it. Twice right.

O Rei do Futebol

I guess one of the advantages of spending some time at home is that you get to explore the inner depths of YouTube to dig up all sorts of things. One popular category I found is famous soccer goals of which there are seemingly endless videos of them, ranging all the way to the 1950′s. One of my favorite “classic goals” scored during a World Cup match was scored by Brazilian player Pelé during the World Cup final against Sweden. Pelé was only 17 at the time and scored 2 of Brazil’s 5 goals for a 5 -2 victory. His first goal during this match is probably one of the most amazing I’ve ever seen and always gives me the jimmies when I see it. In the goal, Pelé is standing in the goal area and receives a pass with his chest. In front of him is a huge Swedish defender, twice his size. Pelé stops the ball, looks the Swede in the eye, does a little kick to lob the ball over him, runs around him and as the ball is coming down on the other side he kicks it in with his foot past the viking goalie for an amazing goal. You can see the whole thing for yourself here:

That being said, this trick of lobbing the ball over the defender seems to be a favorite of Pelé. Digging further in the YouTubage I found this amazing clip from a game from 1959 in which teenage Pelé is playing for his local Brazilian league team Santos. Here, after receiving the pass he does not one, not two, but three consecutive lobs over the defenders heads without the ball touching the ground. During the last lob, he fakes out the goalie and uses his head to score. Fucking amazing. This has gotta be one of the greatest goals I have ever seen. Here is a little clip (they’ll show the goal in the second half of the clip):

So there you have it. Two amazing goals by an amazing player. However, I can’t write a post about goals without showing you another of my all time favorites: Maradona scoring against England in the World Cup in Mexico, in 1986 where he singlehandedly dribbles the ball past what seems to be the entire British team. Check this clip out, the Argentinian announcer sounds like he has just seen God:

The Worst Thanksgiving Ever

I’ve been debating for a bit now whether or not to write this post. In the end I figured that in order to continue blogging in any way that is meaningful to me, I should. Initially it was going to be longer with little observations along the way, but I think  a short version should suffice, for now.  So here it is:

I was actually quite thankful that we had made it to New Jersey the day before Thanksgiving in less than three and a half hours. The idea was to spend a couple of days visiting family and head home on Friday. My family and I had been getting over a series of cough/colds over the last few weeks. On Thursday I had hurt a rib coughing and was in quite a bit of pain for the ride home. Friday night my cough got worse and in the morning, to make a long story short, I went to the emergency room. I was given a chest X-ray and confirmed that I had pneumonia. Unfortunately they also found that I was very anemic, blood counts were off and my spleen was the size of a football. So I was admitted, pumped full of antibiotics and let out after almost a week. I also learned that I apparently have a slow-growing form of lymphoma, which I’ve likely had for a while. Bummer.

The good news is that this disease is supposed to be highly-treatable (I already started) and several new drugs are available, I have access to good doctors at a a major research university, and so far I feel fine, other than a bit winded from recovering from pneumonia. So that’s the news. Right now I’m taking things day by day, and things have been hard on me and my family. Needless to say I’m scared. Something like this definitely changes one’s perspective and priorities.

Since I started my blog, I’ve found it very therapeutic to write about things on my mind, and as opposed to, say, keeping a journal, its nice to get feedback and be forced to crystallize what I am writing since I know others will be reading it. So I hope to continue blogging throughout all of this, mostly about the usual stuff, maybe occasionally about being sick, but I promise I will not make this blog depressing. As long as the blog is helpful to me, I’ll continue to write here. Expect the same kinds of posts, with the same kind of humor (maybe a bit darker) and the usual shenanigans.

One thing for sure is, I’m staying the hell away from fucking New Jersey.

Scoopage

After a few days of peace and quiet, the folks in my lab are starting to trickle back from the Society for Neuroscience annual meeting. Today I had this conversation with my grad student after he returned from the meeting:

“OH MY GOD!!! We need to get my paper published NOW, there was a poster at the meeting describing the exact same experiment as mine, they’re breathing down our necks and… they’re German!!”

“Whoa now, Hobo Joe, tell me what the poster was about…”

“Well they are working on the same neurological condition we are and they also applied the treatment twice and the results were the same as mine, and they did the same thing, with the double treatment and we’re TOTALLY SCREWED!!!”

“Yes, but what was the point of their experiment, what was the question?”

“Um…”

“OK, let’s look at the abstract, what lab was this?”

“They were German.”

So we finally find the abstract and read it over, calmly.

“Dude, did you actually read the poster, or did you just read the title, the first panel and then freak out?”

“Um…”

“Because this has nothing to do with what you are working on, at least not more than in a very superficial way. Sure, they are working on the same condition like another three-thousand people are, and they did apply the treatment twice, but they’re not even close to doing anything that resembles your project.”

“Um… but they were… German…”

This led me to think about scooping. Not the kind that I do after I walk my little mutt every morning, but scientific scooping. The question is, how likely is it really that one’s project might get scooped by another lab, and more importantly, does it really matter? In certain types of scientific research where there is a single answer to a question, such as a crystal structure to a protein, or a specific receptor to a ligand or a gene sequence, I guess scooping would matter. Particularly if you want to be able to say, “Wooohooo! We were the first to describe the structure of blah, blah, blah…” By this point, the contribution of the lab coming in second place would not be that significant. But most science is not really like this. Usually, one is either describing a complex process, or testing a series of interrelated hypotheses, and there is lots of room for different approaches, methods and even answers. Unless it is a very low-hanging fruit, the chances that two labs are doing the same experiment in the exact same way is extremely low. And in fact this is a good thing, because (assuming both labs are competent and good at what they do) that means that the different labs will validate each other’s results, using slightly different approaches, making the discovery more likely to be significant and true. And if one lab does it better than the other, then even if that lab published second, that lab’s paper is likely to become the go-to citation for that finding.

I remember when I first joined PhD lab, my advisor showed me a paper with a very interesting finding, published in a very crappy (and I mean crappy) journal, with somewhat crappily-done experiments. He said, “to start, why don’t you repeat these experiments?” I said, “but why, they’ve already done it?” He replied that “yes, but it is a potentially very interesting finding which, if true, could change the way we think about our field, but I don’t really believe the results. If you are able to replicate them, and extend them, not only will you kick-ass thesis project, but will be able to get some kick-ass publications.” And he was right on both counts. And I was surprised that we were able to publish this in a high profile journal even though we explicitly stated we were not the first ones to discover this phenomenon.

So if you find out a competing lab is working on a similar project, should one be worried about being scooped? In most cases, if you are working on a complex enough problem, I think its worth making sure your science is as strong as possible, rather than rush to publish something that is suboptimal just to beat a competitor. Because in the end the best science will have the most lasting power, and nobody will care if it came out in 2010 or 2011. If you are chasing down a receptor or a really obvious experiment, or your competitors are German, then maybe you should panic.

As far as my student, he should get his paper out anyway. Maybe I should have let him panic a bit more.

Scoopage in action.