Archive for: November, 2011

Spacing Out

Nov 28 2011 Published by under Uncategorized

We spent this Thanksgiving in a quiet northernly locale with a few friends. It was low key and relaxing. Since clear skies were forecast, I thought it would be fun to bring over a small telescope I have and do some stargazing. Full of turkey and other goodies, we headed to a clearing where we could see the night sky. It was dark. It had also snowed the day before and the ice was melting and falling in chunks from the trees that surrounded us, making plopping noises that would occasionally freak us out. The Milky Way snaked its way across the sky  and there was a shitload of stars. Jupiter was high in the sky and was super bright. Using a high-magnification eyepiece we peered at it and you could clearly make out the four Galilean moons – Europa and Io on one side, Ganymede on the other and Callisto dangling right next to the planet. You could also make out the bands on Jupiter's surface. Galileo found these moons in the 1600's and described them in his book Sidereus Nuncius, so it was cool to replicate some 17th century science. We could even make out three of the moons with binoculars.

We then pointed our telescope West, somewhere about half way between Jupiter and the constellation Cassiopeia, above Pegasus, where we found the Andromeda Galaxy. The Andromeda Galaxy is the closest spiral galaxy to the Milky Way, about 2.5 light-years away, and is roughly of about the same size. Even thought it is bright, I had always had trouble spotting it from urban locations due to light pollution. And every time I'd found it, it looked like an unimpressive smudge. But where we were you could see it with the naked eye and was impressive even with binoculars. On the telescope it was beautiful. I used a 35mm eyepiece to get a wide view and even then it barely fit in the field of view. You could even make out some detail in its structure, which was groovy.

Next up, was the Pleiades. The Pleiades is a star cluster which can be found by tracing a straight line from the direction that Orion's belt points to. The Japanese named this cluster Subaru, thus the logo in Subaru cars. With the naked eye most people can see 5 or 6 stars (I just see a blur) but with a telescope you can resolve hundreds. This was also one of  Galileo's observations. The Pleiades are actually prettiest when seen with binoculars, since you can fit the whole thing into your field of view.

The Pleaides, by Galileo. From Sidereus Nuncius.

By then we were getting cold, so we ran inside for a few sips of bourbon before heading back out. When we returned, Orion was high in the sky, offering a nice view of the Orion nebula. If you look at Orion's belt, there is a smudgy-looking thing right next to it, where his sword or whatever would be. That is the Orion Neubula, which is an area of massive star formation. Again, this object is pretty impressive with binoculars. With the telescope we could sort of see the trapezium, which is a small cluster of stars contained within the nebula.

Finally, we aimed our scope at Betelgeuse. Betelgeuse is a red supergiant star. It is huge, if centered within the solar system, its size would reach roughly the orbit of Jupiter. To find Betelgeuse, look perpendicular to Orion's belt. On one side you will see a bright blue star named Rigel. On the opposite side is a bright red star. That's Betelgeuse. In the telescope, Betelgeuse stood like a flaming red ruby in the center of a field of stars, staring back at us from 640 light-years away (now I'm getting all Carl Sagan-y), making a nice conclusion to our viewing session.

I first became interested in amateur astronomy during graduate school. During this time there were two very bright comets which showed up in the sky: Hyakutake and the somewhat less impressive Hale-Bopp. A friend recommended using binoculars to see them and I was impressed how much detail you could actually see. Then I was taking a microscopy course, and the professor showed some pictures he took of the comets with a telescope he built himself (a 16-inch reflector, he even ground his own mirror). The pictures were some NASA-quality shit. This totally sold me. So I got a subscription to Sky and Telescope, bought a copy of "Turn Left at Orion" (highly, highly recommended – this is the most useful observing handbook ever) and got myself a $50 pair of binoculars. It is quite impressive what you can spot with binoculars once you know where to look. A cheap pair of binoculars is far superior and has a better field of view than the telescope Galileo used. So you should be able to see Saturn's rings, craters on the moon, Jupiter's moons, etc. with your binoculars. After a couple of years I'd saved up some money and bought a 6-inch reflector and soon after a used small 3-inch refractor (which is much more portable). Since I had kids and started my job my astronomy hobby has gone somewhat by the wayside, but after this weekend I was inspired to pull out the big scope and start observing again. If you want to get hooked to, next time the moon is  at it's half, go outside and look at it with your binoculars. You'll be impressed, trust me.

7 responses so far

Lab-a-roni and Cheese

Nov 21 2011 Published by under Uncategorized

Recently I was having a conversation about how many things one finds around the lab could be quite useful in the home. For example, parafilm seems like a much better substitute than your typical plastic wrap, and is probably even biodegradable. Those 50 ml conical tubes would be great for storing spices or as little travel containers for shampoo. This led me to thinking how I could concoct a meal in the lab with available equipment, and so I bring you a recipe for a delicious Lab-a-roni and Cheese, complete with catalog numbers:

First make a béchamel sauce. Melt 4 tablespoons of butter in a 100 ml flask over a gas bunsen burner (VWR 89038-530). On a stirring hotplate (Corning 6795-420D) warm up 2 ½ cups of milk in a 500 ml beaker (Corning 1060-500). In a separate hotplate transfer the melted butter to a separate 500 ml beaker and set to heat gently. Slowly add 2 tablespoons of flour to make a roux, stirring with  a 5 ml disposable serological pipette (Fisher 13-676-10C) until it is bubbly and begins to brown a bit. While stirring add the hot milk slowly to the roux making sure it does not get clumpy. Add a large magnetic stir-bar (Fisher 14-513-67) to the sauce to stir and heat very gently. Take 250 grams of sharp cheddar cheese and shred it in a lab blender (Waring 710S) at low speed. Add about half of the cheese to your sauce. Add NaCl (Sigma) to taste to your sauce and 1g of cayenne pepper as well as some black pepper which you have just ground using a glass tissue homogenizer (Potter-Elvehjem 07-358029). Keep the sauce on low, with stirring on. Meanwhile fill a 4 liter glass beaker (Corning CG-8048-4L) with water and 10g NaCl and set to boil on a hotplate. Cook 1 box of pasta (De Cecco No.97) until slightly underdone. While the pasta cooks use a large microtome (RMC Products, Rotary Microtome MR2) to make 1 mm thick coronal slices of Genoa salami. Make about 10 slices. Cut the slices into thin strips with a No.10 scalpel (Fine Science Tools).  Drain pasta using the wire top of a rodent cage (Alternative Design # WL76F) suspended over the sink. Put the cooked pasta in a glass tray (Corning 3175-7) and add half the cheese sauce. Add half of the remaining cheese in a layer, then add another layer of pasta and the remaining sauce. Arrange the strips of salami on top. Cover with the leftover cheese and add some more ground pepper. Put tray in a dry-heat autoclave (Graham FIeld 8376) at 180°C for 20 min. Use a portable bunsen burner (Fisher 14-648-15) to brown the cheese on the surface. And there you go!


Please note: This is only a parody. I do not actually condone trying this in your own lab, don't blame me if you destroy your lab equipment, get cheese all over the autoclave or if you get kicked out for bringing food into the lab. However, you can try this at home, with regular cooking supplies, and make yourself a delicious dinner.

8 responses so far

State your business

Nov 15 2011 Published by under Uncategorized

I was just visiting the International Spy Museum while taking a break from the large Society for Neuroscience meeting.  I was a bit disappointed with the hokeyness of it, but it was fun seeing real spy gadgets from the 40's to the 70's involving dart-shooting umbrellas, film cameras hidden in pens and buttonholes, radio transmitters in shoes and a German WWII Enigma machine. I also liked the fact that at some point the Russians had created a cipher based on an obscure science fiction novel that nobody had read. I think the interactive exhibits could have been made more engaging and not quite as dumb. All in all it was fun, and the little stories about different modern-day spies and how they were caught set me thinking about how we create our identities. Which comes to the real point of my post. As a starting scientist, how do you create an identity? How do you let people know who you are. Of course one is through publishing papers and presenting at meetings, but often people forget presentations and may only get to know you by name. My postdoc actually had a creative idea.

A few weeks back we were having a conversation in the lab about business cards. I personally never use them and don't really know many other scientists that do. The postdoc wanted to know whether it would be a good idea to make cards to hand out during the meeting to people he met. While some people thought that this would be kind of cheesy, and that too was my initial reaction, upon second thought it seemed like a great idea especially when trying to network and get yourself known, particularly if your training was abroad and you really are almost a complete newcomer. So he had some cool cards made with some background design that looked like old histological staining, an old-fashioned drawing of our model organism and some cool looking figure showing some of his data. Then it just had his name, his degree, institution and email. I thought it was brilliant. That way people not only have his contact info but also lots of context that reminds them of the conversation, as well as a cool looking card that you're not prone to just throw away.

So what about you? Do you use a business card? Is it plain, special or covered in rainbows and unicorns?


12 responses so far


Nov 13 2011 Published by under Uncategorized

One thing people don't tell you about tackling big meetings, such as the Society for Neuroscience where I'm currently at, is that one has to perfect the art of looking without looking. That is, when you have a list of about 20 posters you might want to visit in the next couple of hours and have to decide which ones to spend time at, chatting with the presenter. But the trick is in making this decision by giving a preliminary glance at the poster without engaging the presenter. Otherwise you might be stuck and, out of politeness, you might have to stick around and listen to the whole 20 min spiel. I usually do a super preliminary walk by and asses whether the person put effort into making the poster. A bad poster most of the time signifies bad data. It does not necessarily have to show aesthetic appeal, but rather that at least some thought was put into it. I also see whether there is too much data. My attention span at meeting is short and I cannot focus on a poster with 60 graphs on it. After the first walk-by I circle around and have another look. I usually wait until the presenter is engaged with someone else so I can casually approach the poster and peruse its results. If its a good poster I can usually get the punchline with a few glances and that usually is enough. I take a few notes and go. If the data is interesting, then I look the presenter in the eye and ask for the spiel. I can usually handle about 6-8 of these in-depth views in one poster session before my brain starts to get sluggish. The rest I give cursory glances and hope I don't get ensnared. That way also whenever I present a poster I just let people know to tell me if they'd like the spiel or have questions, that way they don't feel pressured to stay.

That being said I saw some great posters today, by many of my collaborators and some by fellow bloggers, where I showed up incognito (sort of). I ran into my postdoc at some point who is attending this meeting for the first time, and his brain looked much more fried than mine. Maybe he doesn't know about the drive-by poster watching technique.

8 responses so far

Choo-choo boogie

Nov 12 2011 Published by under Uncategorized

Well, I'm on my way to the annual Society for Neuroscience meeting in DC. Because I procrastinated until the last minute and couldn't find cheap tickets with reasonable travel times, I decided to take the train, which all in all does not take that much longer than flying. And you don't have to deal with airport security and other annoyances. Now here I am, sipping my drink , enjoying the free WiFi and watching the scenery zip past. There's definitely a very different crew of people on the train that the ones you typically meet on a plane. Instead of the harried and disheveled cranky plane travelers, people here seem a bit more diverse. There was the dude that walked past dressed like Brad Pitt in that movie "Inglorious Basterds" with the stupid mustache and all. Or the woman covered in sequined clothing, head to toe, carrying about six hundred laptop computers, cell phones and other strange electronic gizmos. Or the six impeccably groomed apparently functional guys that walked in together, following instructions from one that appeared to their leader and kept telling everyone where to sit and then started handing out snacks for them all. FIrst apples, then power bars. Or the Eastern EUropean-sounding dude that walked in and pulled out an enormous book about Rembrandt from his bag, and then promptly got kicked out of the train by the conductor for not having the right kind of ticket. There's also a little kid screaming up the aisle, but as long as its not my kid, that never bothered me, and at least he can run amok up and down the aisle.

Plus you don't get hit in the head with random people carrying their poster tubes around the airport.

Hopefully the meeting will be good – 30,000+ people is always difficult to manage. If I get a chance I'll post a picture of the sea of posters for anyone who hasn't attended this kind of scientific meeting.

No responses yet

Slip 'n' slides

Nov 09 2011 Published by under Uncategorized

Dear Students,
I've noticed a trend among grad students when preparing slides for their presentations that there is a tendency to spend lots of time making the slides pretty, but giving little thought to how well a slide conveys the content of the information it is supposed to convey. Cramming about 5 graphs into one third of the usable space in a slide (leaving the rest for superfluous "design" elements) not only makes the slide difficult to digest but also shrinks the figure's text to an impossible-to-see size. Please get out of the habit of doing this if you want your professors and fellow students to stay awake during your talk and not be fantasizing about jumping out the window. If you are unsure whether your slides are up to snuff, I'd be happy to take a look at them a few days before your talk and give you some pointers.
-Cranky Prof. N

5 responses so far

Daylight savings denial

Nov 08 2011 Published by under Uncategorized

I always find it kind of annoying that daylight savings time ends on a Saturday evening, basically your extra hour of sleep is wasted on Sunday which you can wake up late anyway, and your circadian-entrained kids will wake you up at the crack of dawn anyway. So I always pretend it doesn't happen, I wait until Sunday night to change the clocks after the kids go to bed. That way you get an extra hour of sleep on Monday morning and everyone is happy. Yesterday I had to wake up extra early to catch a train, thanks to my denial of the time change I was able to wake up at a normal time. Now I'm thinking that every Friday afternoon I will push all the clocks at home one hour forward, send the kids to be early and then regain the hour on Sunday night, ensuring an extra hour of sleep. Who cares if you're in sync with the rest of the world, right?

5 responses so far

Calaveras 2.0

Nov 02 2011 Published by under Uncategorized

In México, November 2 is Día de Muertos or Day of the Dead. One venerable tradition is to write little obituaries for living people you know with a little skeleton of themselves, or a sugar skull with their name to accompany it. Newspapers will write funny obituaries, usually in verse of politicians and other public figures. These fake obits are known as "Calaveras". Last year I wrote some calaveras of a few fellow science bloggers. To continue the tradition I'm happy to present a new set of calavers of some fellow bloggers I've had the pleasure to interact with in the previous year. Enjoy!

La Doctora Becca, RIP

So sad, la Doctora Becca is gone.

She thought her new lab was all done.

So she designed a new cocktail,

just as her gas burner read "fail".

The explosion lifted the lab right off the ground,

And no traces of Dr. Becca or the cocktail were ever found.

Zen Faulkes, was not Guy Fawkes

Poor ole' Zen Faulkes.

He met his demise when they confused him for Guy Fawkes.

He said "You got the wrong guy, I study crayfish!"

But they just thought he was being all selfish.

From the bonfire he yelled "No, really, look at my poster!"

But that didn't work, they thought he was just another imposter.

GertyZ had too much cerveza

Our friend GertyZ has passed on while drinking cerveza.

She had one too many, fell and hit her cabeza.

At least it was microbrew and not a Budweiser.

But she should have looked where she was going, that would have been wiser.

5 responses so far

The butcher, the baker, the candlestick maker...

Nov 01 2011 Published by under Uncategorized

I've mentioned before that running a lab is like running a ship. For the most part it's like running a sinking ship which you are frantically trying to keep afloat, but the analogy extends further. And maybe here's where the analogy can diverge depending on how you run your lab. In many large ships you have a crew of specialists. One can navigate, another steers, others fixes sails, others keep the cannons in shape, a bunch of lackeys will swab the decks and coil the ropes, someone cooks, that sort of thing. The captain's job is to set the course and make sure everyone gets along and does their job, the goal being to get to where they need to get, and deal with any trouble along the way.

This can be an efficient way to run a lab. You can have a bunch of specialists all working on different aspects of a core project. The molecular biologists are running the DNA chips and generating the transgenic animals, the imagers are working the confocal microscopes, the electrophysiologists are cranking along in their rigs, the engineers are devising new devices, the spies are infiltrating competitor's labs, the programmers are modeling your data and the nuclear physicist is plotting the global takeover. This division of labor ensures a steady throughput of papers and allows the lab to efficiently take new directions and tackle new projects. So from an efficiency perspective, this is the way to go.

What is less clear is what the contributions of the first authors on these papers is. If everyone is a specialist, what makes someone first author? Also, to me the training potential of these labs seems questionable. How can you be expected to run your own lab if you spent your postdoc doing the same thing over and over? Probably someone who is smart will pick up things along the way and by observation learns how shit gets done. But many people will be headed to nowhere, despite their first author paper on some fancy glamor journal.

So there's an alternate model, a model where people are assigned projects and they are then responsible for everything in the paper. In this model, some people are better at some things than others, but everyone then gets a chance to learn and do multiple techniques. So if your project requires imaging, genetics and behavioral testing, then you learn to do all these things by talking to the folks in the lab that are experts at these techniques. And if you don't want to learn a new technique, then you are responsible for arranging some sort of internal collaboration. In this way everyone mentors each other and learns about each other's projects, as well as learns how to put the big picture together. While this may cause papers to take longer to finish, I think that over the period of 3 years or so the total output of the lab is comparable to the previous model. It also ensures that say, the expert in time travel leaves your lab, then you are not left high and dry until someone else figures out how to run the Neutrino Hyperaccelerator so you can go back in time and submit before your competitor does.

I'm not sure which model is better overall. I did my postdoc in a lab that ran using the second model and that is mostly how I run my lab. I try to get everyone to learn and use multiple techniques and to pilot their own projects. But I see the merit of both approaches. Any thoughts?

Image: B. Powis

5 responses so far