I've been really busy of late. Over the summer I have been mentoring two students, Gloria who sadly left us for Danesh Moazed's lab (a great choice if you ask me) and Lesley who will be leaving next week to work in a lab at Duke. I have also been busy with the RNA Data Club - last week we had our first meeting outside of Harvard Med School, at the Whitehead Institute (thanks to Christina Mayr and other members of the Bartel lab). Next Month we'll be have over speakers from Pam Silver's group and our first Yalie, Navtej Toor from the Pyle Lab. Next week, Jenni and I are moving to a new…
Maybe this will become the new Friday feature at The Daily Transcript ...
If you are a scientist, I urge you to listen to the commencement speech that Krulwich gave to the Cal Tech graduates earlier this year.
Check it out. ht: Dan @ BitesizeBio
Sorry, I've been busy these past few days. I want to respond to a comment posted by Dan and take this opportunity to broaden the discussion about how we use language to construct models. Dan's concerns about information and life have been echoed by many out there, for example by John Wilkins. Can we use the term "information" when discussing life? Is there such a thing as "information"? Are these buzzwords without any deeper meaning? What is lost in such an analysis is that all of our theories are infused with metaphors. These words and concepts help us to better understand the ideas and…
A pocket-size lensless microscope that uses on-chip optofluidic microscopy (OFM). The sample is dragged in front of the detector and an image is extrapolated. Now imagine if every cell phone had one of these? Ref:Xiquan Cui, Lap Man Lee, Xin Heng, Weiwei Zhong, Paul W. Sternberg, Demetri Psaltis, and Changhuei Yang Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging PNAS (08) 105:10670-10675 Update: someone just informed me of this interview of Changhuei Yang on NPR, click here to listen.
I was going to write something about the latest analysis of NIH funding in Science, but DrugMonkey did the work for me so go read his post. The bottom line is that NIH funding goes through boom-bust cycles that cause instability throughout the biomedical fields. In boom times the biomedical research fields recruit lots of grad students and postdocs (many of these recruits being foreign), after all the PIs need the work force and they now have funds to pay them. Then when these junior scientists go looking for their own lab and their first R01, the lack of funds forces many out of academia. To…
Here's an interesting micrograph of a nucleus lit up by fluorescent dextran. Besides the slightly darker areas (these are nucleoli - dense structures where ribosomes are manufactured), you'll note the small round blebs on the top of this dumbbell shaped nucleus. I run into cells like this once in a while, and I'm sure that others have seen similar nuclear morphologies, yet we still have no clue how such structures could form.
Two weeks ago, an interesting commentary by Paul Nurse, came out in Nature. The bottom line? We need to change how we study and understand cellular signaling cascades. First, some background. Cellular function is governed by a network of protein interactions that act like an information processing device. These devices sense external inputs, such as cell signaling factors, pH, nutrient availability and temperature, and they regulate a vast number of different cellular responses such as changes in morphology, alterations in the metabolic state, the modulation of cell division, or the…
My iPod has been a great addition to my life. I use it to listen to podcasts and audiobooks on my half-hour walks, to and from work. But recently two of my favorite items have gone into suspended animation. The first one is my absolute favorite podcast, The History of Rome, produced by Mike Duncan. Starting from its mythical beginnings as told in the Aeneid, Roman history was delivered in 15min segments to my iPod every week. Mike had been producing these for a year now (yes, that makes almost 50 episode). In the pocasts we encountered the Etruscans, the Samnites, Cincinnatus, Hannibal,…
As a scientist, I traffic in data, ideas, models and theories. I spend a lot of time thinking about how the whole process works. And many scientists and science philosophers have thought about this as well. One inescapable fact: humans tend to duck, deny and fool themselves into believing certain ideas even when data points the other way. It's the little voice in our head that says "I am not biased, it's everyone else." Humans are highly prone to much cognitive dissonance. It's just that in science you must confront this reality head on, all the time. These tendencies exist everywhere and are…
Now that I have a good chunk of time where I'm not scheduled to run off to some distant land for vacation or to give some talk, I have decided to work extra hard. Right now I'm incubating my samples. This post is the result of me killing that time. I want to bring up an article that appeared n WIRED over a month ago. I know, that's ancient history in the world of blogs, but it's an idea that pops up once in a while and it is common in certain young naive scientists. Let me just quote a passage from the article: This is a world where massive amounts of data and applied mathematics replace…
I have a favour to ask of all of you. Go and fill in SciLink's Tree of Science (you'll have to sign up to SciLink first). Why? Well it is very interesting to see how different scientists are connected. And on top of that we can settle a longstanding dispute - what is the appropriate Erdos Number for biologists. You might be asking, what is the Erdos Number? or who was Paul Erdos Number? From an old post by RPM: Paul Erdos was an extremely prolific and mobile mathematician who has left a legacy in academia in the form of the Erdos Number -- a count of your "academic distance" from Erdos.…
If you are a postdoc or a junior faculty in the biomedical sciences, you have probably seen this infamous cartoon by Dent: Yesterday I was talking with my good pal Dan and we were discussing a few other great pieces by Dent. After that conversation, I did what anyone else would do, I Googled the guy. Little did I know, I had just stumbled into a gold mine! Here it is: http://dentcartoons.blogspot.com/ Proceed with caution.
We were planning to head to Europe so when I discovered that the cheapest tickets were being offered by Icelandair, I jumped on it. Why? I have always wanted to visit this mystic land and Icelandair lets you have a free stopover for up to a week. I highly recommend that you do this once - Iceland was far and away the highlight of our European trip. Day I - We arrived late in Keflavik where the main international airport is located. This is on the southwest corner of the island and lies right on top of the mid Atlantic ridge in an area known as the Reykjanes. Already you can see that Iceland…
I've sign into yet another sciency LinkedIn type site. This time it's Epernicus. I've had a good look at the site, it's about on par with SciLink with some exceptions. 1) The scientific genealogy application on SciLink is much better then that on the Epernicus site. Why? You can extensively modify the tree beyond your own personal connections. Bigger trees are better (more info). 2) The profile page of Epernicus lists all your publications in chronological order - SciLink take note. So by my quick score it's 1-1. I guess like every other epic battle (VHS vs. Beta, HD DVD vs. blu-ray and AC…
A friend of mine just sent this to me (for the record, he's a structure biologist, i.e. he studies the structure of proteins and other biological molecules): My kid had a screen session with a school administrator for his kindergarten today. Following are some answers he came up with: Teacher: "What is your favorite activity?" Son: "Thinking." He is probably right. He is always thinking of how to get his favorite food: rice krispies, candy... Teacher: "What does your Daddy do?" Son: "Work." Teacher: "Where does you Daddy work?" Son: "I don't know." Teacher: "What's your Daddy's job?" Son: "…
Inspired by a conversation with Awesome Mike. Your science career, what type of video game is it? At times it might resemble a labyrinth full of demons that you must slay. (Or maybe it's like Grand Theft Auto? Well since I've never played that game nor Halo, I'll stick to the metaphorical game that's running through my head.) Level 1: Undergraduate The first level is the easiest. Stay focused and you'll get to the end. Final monster at the end of the round? Those exam finals? Psht. Level 2: Grad Student This level bit trickier then the previous one. The first major obstacle is choosing the…
After Paris we flew to Munich on Airberlin (20 Euros per ticket, 50 Euros after taxes and airport fees.) There we met up with some former colleagues (Julia and Michael) and a current member of the Rapoport Lab (Briana) who will be leaving us soon to start her own lab in the MCB department at Harvard's Main Campus. Also in attendance was Briana's husband and my wife who snapped this picture of us in the English Garden. Munich is a beautiful city. For anyone who enjoys the music, Munich might as well be the world capitol of classical music. The number of great performers who currently live in-…
We then arrived in Paris on June 21st. If spending the summer solstice in the city of lights means nothing to you then you've never heard of Fete de la Musique, a one day outdoor party. The streets were filled with Parisians taking in the food, the sights and the sounds generated from live musicians trough out the city. Fete de la Musique is now celebrated in almost every part of France and a good chunk of Switzerland too. There were teenage garage bands, DJs, tam-tam players and of course many troubadours. At one location the musician's distributed lyrics into the crowd so that everyone…