Grant me some science

(by namnezia) Jun 27 2013

I've been spending the last few weeks teaching in an intensive summer course in my field. This involves spending long hours in the lab teaching teaching eager grads and postdocs how to do the latest techniques, and every time I do this I'm reminded of how fun it is to do labwork. So far we've tested some new ideas, some better than others, and I've come up with a bunch of cool follow-up experiments to do at home. Unfortunately, I doubt that I'll actually get around to doing those cool experiments, since at home I don't really get much of a chance to spend time in the lab. What do I do? I write grants mostly. Which is silly, because a job that nowdays requires you to spend 75% of your time writing something that has a 90% likelihood of going unfunded is basically a waste of time. Time which could be better spent actually DOING science, writing papers and actually learning something.
So how can we improve this? I can't really write faster than I do now, I'm quite saturated on that front. Funding isn't going to get better and a systemic fix is unlikely to happen soon. Crowdfunding one's science is just a silly idea that's not sustainable in the long run for supporting a lab and staff, and which anyway would also take a huge amount of time. So what's left is to improve the efficiency of the grant submission and writing process. How? Hire someone to write the grants! Although I've never met one, nor do I know anyone who's used one, allegedly these people exist. Wouldn't it be nice if you could sit with someone for a couple of hours and outline some experiments and point them to relevant background material and then they go and write the thing for you? The ideas would still be yours, just the actual writing is done by someone who is a trained writer, who can put things much more clearly and eloquently than you can. Someone who can make your science sound exciting! And I don't want someone who will read and edit my grant, this takes twice the time. I want someone to just write the damn thing and hand me a polished draft. This would ideally be a person with a PhD in science and some sort of writing degree or professional training. And I think University grant offices should pay for these people's services. It's to their benefits that PI's send higher quality grants AND also have time to do high-quality science. Rather than playing the mostly bureaucratic and sometimes obstructive roles in the grant submission process, grants offices could become hotbeds of creativity, productively cranking out grant after high-quality grant proposal.
But of course that's just a pipe, dream. I should stop procrastinating and go back to working on my grant. It's due on Tuesday.

6 responses so far

Stacks on shelves

(by namnezia) May 08 2013

OK, listen up kids! If you are taking something from a shelf and there's other stuff on top of it, the best way to do this is to first remove the stuff on top, take what you need and put the stuff you don't need back where it was. This is superior to simply yanking out what you need and letting all the other stuff spill all over the floor and then walking away. This useful bit of knowledge can apply to lots of things, including books, clothes in your drawers, dog food, toys, dishes and snacks! So now you know. You may now go about your business (after you pick up the friggin' mess you made in your bedrooms).

4 responses so far

Come in, we're open!

(by namnezia) May 07 2013

A lot of the push from the open access (OA) movement is to make federally-funded scientific research freely available to the wider public. This of course is a laudable goal, especially since this research is the fruit of taxpayer money. What I decided to do is to ask myself the question, what if I wanted to access the latest biomedical research but was not affiliated with a university or medical center? What would I have access to? For the last five years or so, the NIH has required that any research that is published as a result of NIH grants be uploaded into a freely accessible database called PubMed Central. This is in fact done automatically by several journals upon acceptance of a paper, such that PMC now has over 2.7 million articles freely available. The one catch, which seems to be more of an issue for some people and not for others, is that in many cases this material is not made available on PMC until after 6-12 months post publication. In fact many top journals are following the trend of offering their archives for free for articles that are 6+ months old. Obviously, open access journals make their stuff available immediately, but these represent a small portion of overall scientific publications. Likewise, many publishers will make their articles available for free for patients researching a given condition.

So, what if you wanted to see what was published in the latest issue of Cell, or of the Journal of Neuroscience and don't want to wait 6 months, what are your options? For one, you could always try a library! Yes those still exist! I decided to check what kinds of resources would be available in several US cities for the general public and found quite a bit. For example, if you live in Boston, and you are a member of the Boston Public Library, you can have free physical access to the Harvard Medical School Library, which means that you can access electronic resources and therefore ay journals the library subscribes to. If you live in New York, the New York Public Library offers electronic access to hundreds of scientific and medical journals. In DC, the National Library of Medicine in Bethesda also offers free access to thousands of online medical journals. OK, but what if you don't live in one of these major cities? Many public universities and medical schools provide free or paid access to their libraries for research purposes, as do many private universities.

We are all so used to being able to access all the information all the time from our living rooms while sitting around in our underwear eating cheese doodles. But in fact if you actually get to a library you will find that you can find and access almost everything you are looking for, even if it's behind a paywall. Ideally, yes, all information should be free all the time, but in reality things aren't quite as bad as some would lead us to think.


6 responses so far

Espress yourself

(by namnezia) May 01 2013

One piece of advice new faculty rarely receive regards something that can increase the productivity, morale and well-being of new lab by several fold. What is this magic bullet? Espresso! That's right, numerous studies have shown that labs that drink lots of espresso publish more often in glamour journals, get more grants and establish new and productive collaborations. This is known. An espresso machine is one of the best investments a new PI can make in their fledgeling lab, and with your new big-bucks PI salary, you can definitely afford to get one.

So, you say, "I want to buy an espresso machine for my lab, I want my lab to be productive, but I don't know what to get?" The choices of machines one can get are overwhelming and the espresso machine world can be confusing and scary for a novice. So I'm going to give you a little guide regarding the types of espresso machines that would work well in a lab environment. I'm not really going to go into specific brands and models, but rather more toward the classes of machines that work well for a lab. There are several aspects that you should consider when buying a lab espresso machine, including: quality of the coffee, ease of use, cleanliness, space and price. The three classes I will review have different pros and cons regarding each of these aspects.

Single-serve espresso machines are the easiest to use. You basically insert a pre-packaged espresso pod or capsule press a button and espresso comes out. Then you just trow out the used capsule and drink away. I think these have several drawbacks, personally I don't really like the espresso they make, to me it always comes out kind of weak and watery in the several machines I've tried. Also the capsules are expensive and not entirely ubiquitous. So if you happen to run out, you cant just run down to the local coffee shop for more coffee beans. For the same reason, it also limits the types of coffee you can use, and you know it's been roasted ground and package a long time ago. They aren't super expensive however, take up little counter space, don't need to be near a sink and the learning curve is zero.

Super automatic machines are a nice compromise. You basically add coffee into a hopper, press a button and the machine grinds and tamps your coffee and pulls the shot for you. You can tweak a few parameters to optimize the flavor and consistency of the cup, but once these initial tweaks are done you don't really need to worry about them and it becomes a push-button operation. It is a bit messy to empty the leftover ground container when its full, so being near a sink helps, like in a common kitchen area. With these, you know the coffee is always freshly ground and you can use any beans you like, from crappy burnt one from Starbucks, to delicious ones from your local roaster. One problem with these machines is that they don't tend to be very good or durable, and if one part breaks, the whole thing is broken. They are also fucking expensive.

Finally, we get to the semi-automatic machines. These are like the ones you see in most coffee shops or in people's homes, but can vary greatly in price and quality. In these, you add ground coffee to the portafilter, tamp it down, put it in the machine and press a button to turn on the pump. These have the highest number of variables, from using the right ground, the right amount of coffee, tamping correctly and running the pump for the right amount of time. As a result they have a steeper learning curve and can result in really crappy espresso, or extremely delicious espresso. They are also messy since you have to empty the used grounds every time, so they need to be somewhere with a garbage can and sink. That being said, I prefer these. Since they don't have to be too expensive to make decent espresso, you can use any kind of beans you like and they are relatively durable and can withstand abuse by multiple people. You could get a nice grinder to go along with it, or have them grind the beans for you at the coffeeshop. Keep in mind that most grinders you find at supermarkets will not grind the coffee finely enough for use in these machines.

For my lab, when I started, another faculty member and I teamed up to buy a decent but reasonably-priced semi-automatic and it has been going in full force for 9 years. I use it a couple of times a day and well as various lab members to different degrees. I like it because it makes decent espresso (even with $3.50/lb cans of Café Bustelo) and has turned out to be quite durable. But if you're not so picky about your espresso and are organized enough to keep a steady supply of single-serve capsules, probably the single serve machines are the best bet for a lab.

So there you go! Invest in your lab! Give them espresso!

Some 'spresso coming up!

Some 'spresso coming up!


7 responses so far

If you would like a recommendation...

(by namnezia) Apr 30 2013

So for ay undergrads reading this, I have some sage advice. If you are planning on asking your professor for a letter of recommendation, try to make sure your professor KNOWS WHO YOU ARE. Simply showing up out of the blue towards the end of the semester and then asking for a letter for Med School/Internships/Study Abroad/ Fellowships/Circus School (really!), etc. will not earn you a good letter if I don't know who you are. At most I can say you did well in my class, maybe asked a few questions, took other challenging courses and that's about it. That's not going to get you the Fullbright. It may seem that after spending a semester listening to me blather on about great moments in science or whatever you feel like you know me, you know how I think, maybe identify with how I think, much like you would with an author in a book. But that doesn't mean I know YOU. If you want that to happen, you need to participate in class and more importantly come to office hours. That's what they're for, to get to know your professors better and get them to know you. Office hours aren't just for asking for clarification of the material, although they can be that too, so take advantage of a good opportunity to get individual attention from you prof, and to make sure that when you ask them for a letter he or she will have something nice and unique to say about you.

5 responses so far

A good day in science

(by namnezia) Apr 30 2013

So I was getting ready to write a depressing post on the tedium of writing and not getting grants and blah, blah, blabbity blah, when I realized that maybe what folks need to read is a good reminder about why science is a great job. So let me tell you about last Thursday. In the morning I gave the last lecture of the semester for my class, and afterwards got some nice thank-yous from the students saying they learned a lot, that they wanted to work in my lab, take my other classes, etc. Afterwards I read some papers from a bigwig that was visiting the department and then met with said bigwig. We had a nice chat and argued about one of his recent papers. Not angrily but definitely heartily. Then an undergrad who's visiting from Hong Kong for the semester and had been working in my lab presented her data in lab meeting and had really promising cool results. Too bad she has to return to Hong Kong, the project will have to be continued without her. Then I reanalyzed the data for a rotation student and actually found that she may have a result (this is after she had been feelin' down that her rotation project had been a waste) and then had a good conversation with her about how to follow up and why she didn't see the result initially and how it fit nicely with the data presented in lab meeting. She seemed much more cheered-up, I hope she stays in my lab even if the result ultimately doesn't pan out because she is great. Then I went to the bigwig's seminar which was awesome and was glad to hear others brought the same objections I had afterwards. I then had a good discussion about the seminar with a colleague I seldom get to see but that I really like. Finally, I was chillin' in my office packing up when my other grad student wanted to talk about his experiments. So we did some statistics on his data and also found he had even cooler results, which led to another good conversation. All in all a fun day spent discussing, analyzing, teaching and thinking about science with intelligent folks. And that is why on days like this I really like my job. Sure, it's rewarding to publish papers and get grants, but it's really the day to day aspects of the job that can really make it all worth it.

3 responses so far

Dumbass 2

(by namnezia) Apr 12 2013

PSA: When sending emails to your entire lab, make sure you don't accidentally use your secret blog email account. Presumably they are all now reading my blog, so hi guys!!

7 responses so far


(by namnezia) Apr 12 2013

I felt so free and easy when I found out my new pants had a discreet dedicated mobile-phone pocket. Until I forgot about it and put my pants through the washing machine.

6 responses so far

Corrida de Guadalupe-Reyes

(by namnezia) Jan 03 2013

A few years ago, I received an email from a teacher in my kids' school:

Hello Dr. Namnezia, I teach French and Spanish at Yourkids' School.  A colleague mentioned you to me as someone who had lived in Mexico. I will be doing a cultural unit next week on the Mexican symbol, La Virgen de Guadalupe, with our 6th grade Spanish class.  We were hoping you could visit the class and talk in English or in simple Spanish to them about La Virgen and what she means to most Mexicans, and also what she meant to you and your family.

My reply was:

Thanks for asking me to talk in your class, and yes, I was born and raised in Mexico City. However, I am probably not the person you want to to talk to your class about La Virgen de Guadalupe, since I am Jewish! (yes, there are Jews in Mexico, and no, they are not all sepharadic from Spain). So "La Virgen" didn't really mean much at all to me and to my family. Perhaps when you do a unit about how Mexican society can be just as culturally and ethnically diverse as that of the United States, I'll be happy to visit.

I have to admit my reply was a little snippy, but I was annoyed at the assumptions this dude was making. However, I have to admit he really did have a point, albeit a small one. See, in Mexico (and in a bunch of other places) the holiday season isn't quite over yet, there's still one more hurrah: Día de los Reyes, or Day of the Kings, also known as Epiphany. This marks the end of what is referred to as "Corrida de Guadalupe-Reyes", which means a bunch of parties that occur between Dec. 12, Day of the Virgin of Guadalupe and Jan. 6, Kings Day. Some take this time as a personal challenge to go to a party and get drunk every day of the corrida. That's 26 days of drinking. Growing up in a heavily catholic country one cannot but help celebrating some of these holidays. Not really as a family, but at friends' houses, and at school, and at friends of friends' houses, and the neighbors, you get the idea. We didn't really do Christmas, or celebrate the day of the Virgin of Guadalupe, but we definitely did Kings Day. Not much in the way of exchanging presents, but in eating delicious Rosca de Reyes. Rosca is a delicious round, fluffy sweet bread, covered in crusty sugary bits alternating with dried fruit. Inside somewhere is one (or many) little plastic doll representing baby jesus. Or Jesús as they say in those parts. Everybody cuts a piece, and whoever gets the doll has to throw a party with tamales sometime in February. Since we didn't do the tamale thing, my goal was to get as many dolls as possible. I think I had collected dozens as a kid. In contrast, my grandfather told me that once he actually made himself swallow jesus to avoid throwing a tamale party. He also told me, since he was fond of talking about such things, that it took three days for him to "pass" jesus.

So, if you are depressed that the holidays are  over, you've opened your presents, ate your fruitcake, lit your Hanukkah candles, stayed up until midnight to greet 2013, given the Christmas tree the ol' heave-ho down the front steps, now's your chance to keep 'em going for a few more days. Get yourself to your local Mexican bakery and order a big Rosca de Reyes. On January 6, eat it up and as a bonus you or one of your friends has to throw a tamale party in February.


2 responses so far

Rita Levi Montalcini and Nerve Growth Factor: Repost

(by namnezia) Jan 03 2013

This last week one of my neuroscience heroes, Rita Levi Montalcini, passed away at the age of 103. In her honor, I decided to repost a post I wrote a few months ago about one of her greatest contributions to science: nerve growth factor. In addition there's a nice profile of her and her work in Nature. Here's the repost:

A Neuroscience Field Guide: Nerve Growth Factor

Nerve growth factor, NGF for short, is a soluble protein that is secreted by various tissues in the body, and it promotes the growth of nerve cell processes and survival of neurons. It is the first of a class of molecules known as neurotrophins which are very important for the development and function of the nervous system.

What is remarkable about NGF is how it was discovered and by whom. NGF was discovered by Rita Levi-Montalcini an Italian, Jewish young doctor. She originally became interested in a set of experiments by renowned embryologist Viktor Hamburger which had observed that removing a limb bud from a chicken embryo caused the sensory neurons that innervated the undeveloped limb to die off. This suggested that there was something about the target tissue that promoted neurons' survival in the embryo.

Levi-Montalcini had just graduated from medical school when Mussolini issued the "Manifesto per la Difesa della Razza", which ultimately led to a ban of all non-Aryans from having professional and academic careers. Undaunted, Levi-Montalcini set up a laboratory in her bedroom in her parents house and then after the bombing of Turin in her family's country cottage. After the War she was invited to St. Louis, MO to join Viktor Hamburger where she remained for many years and where she performed her Nobel Prize-winning research.

One of her initial observations was that if you implant specific mouse tumor cells on a chick embryo, sensory neurons will grow rapidly and sprout new axons which will innervate the tumor cells, again confirming that certain target tissues can promote nerve growth in embryonic tissues. The question was how did the target tissues do this? The key experiment came when she and her colleagues grew on one end of a cell culture dish some of these mouse tumor cells, and on the other a bit of neural tissue known as a sensory ganglion. After a few days, she observed that the neurons in the sensory ganglia grew a bunch new axons, and these axons seemed to be oriented toward the tumor cells. As if they were being attracted. This told her that the tumor cells were actually releasing some soluble factor into the growth media. The factor promoted growth of nerve cells and helped them live longer in a culture dish. This factor was later isolated by biochemist Stanley Cohen and shown to be a protein which they dubbed, imaginatively, nerve growth factor. Both Cohen and Levi-Montalcini received Nobel Prize in 1986.


From Levi-Montalcini's Nobel Lecture: Drawing of the cell culture experiment. The tissue on the left is the mouse tumor cells, the tissue on the left is the sensory ganglion. Note the axons growing out towards the mouse tissue.


How does NGF work? Now we know that NGF, as well as several other similar proteins known as neurotrophins, activate receptors in target cells which are called tyrosine receptor kinases, or Trk. Trks are proteins which are on the surface of neurons that when activated by NGF cause a series of cellular processes which cause embryonic neurons to grow new axons and to survive. Any cells which do not find their target will undergo a self-destructive process called apoptosis, thus help in the developing nervous system keep appropriate connections and eliminate inappropriate ones. Furthermore, NGF could form the basis of new therapies for treating various degenerative brain disorders and maybe promote neural regeneration after injury.

Rita Levi-Montalcini is now 103 years old, the oldest living Nobel laureate. Apparently she uses NGF eye-drops daily (it's true!).

Rita Levi-Montalcini in 2009, at her 100th birthday party.


Further Reading

Rita Levi-Montalcini Nobel Lecture and her Autobiography

Stanley Cohen Nobel Lecture


3 responses so far

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