lab life
apalazzo | December 4, 2006The H-index was the brainchild of Jorge Hirsch. It's a method to quantify a researchers impact. (To read more on this, check this entry of mine: What's your h-index.)
I was just alerted that Michael Schwartzbach has written a program that can calculate your very own h-index quickly over the web by hacking into Google Scholar. I tried using it to get mine ... unfortunately "A Palazzo", is not unique and so I couldn't recalculate my own h-index. I finally got it to work by typing "A Palazzo" and Columbia and got 8 (the value I had the last time I checked). Go visit Epidemiologic Inquiry to use…
apalazzo | November 26, 2006Thursday, my wife and I hosted our annual Thanksgiving for the left behind. Every year, we gather all the foreigners and Americans who couldn't make it back to their own family and have a great big feast. This year, we stuffed 14 people into our small apartment and had a ball. This is the 7th year we've held our left behind Thanksgiving, and since my wife's brother and his wife moved to Boston we had family over as well.
We've been slowly recovering from the big party. It took about a day and a half to prepare the meal, and after the event it took another day to clean the place and an…
apalazzo | November 20, 2006It looks like Tonegawa stepped down as head of MIT's Picower Institute after the kerfuffle over his emails to Alla Karpova, who was offered a job at MIT's McGovern Institute. Read the article in today's Boston Globe: MIT neuroscience center head quits.
On the one hand those emails, although PC on the surface, were pretty nasty between the lines.
On the other hand I've heard that despite his public persona, he's really a nice guy (according to his lab members).
[HT: Zuska.]
apalazzo | November 13, 2006Working in a lab for too long and you'll acquire a type of lingo that we call "X-speak". It happens to everyone you borrow words used within one environment and apply them to other situations. With so many members of our lab preparing solutions we (as I'm sure many of you) many here are fluent in X-speak. This is exacerbated by food preparation:
"Do we have any chicken broth."
"Yeah, it's pretty concentrated, it's about a 100X stock."
"I see that would explain why it's sold in such small aliquots and why it is gelatinous at four degrees."
"Right, just remember to add enough water to get the…
apalazzo | November 9, 2006Ever tried. Ever failed. No matter. Try Again. Fail again. Fail better."
-Samuel Beckett
apalazzo | November 3, 2006I didn't blog about this when it first came out, go see Janet Stemwedel's blog (here, here and here) on how Susumu Tonegawa dissuaded Alla Karpova from taking a position at MIT.
Here's the latest from the Boston Globe:
Susumu Tonegawa , whose actions sparked an outcry from several colleagues, will not be disciplined, L. Rafael Reif, Massachusetts Institute of Technology provost, said yesterday. Reif said several individuals acted inappropriately in the failed effort to recruit neuroscientist Alla Karpova , and there is no need to punish anyone because the real blame lies with the competitive…
apalazzo | November 2, 2006I know that we have NCBI etc. but couldn't someone construct something close to the Yeast Genome Data Base for the human genome??? This site rocks.
(P.S. Yes probably ENSEMBL is the best pan genome bioinformatics gateway, I'm exploring it now. Hmm. So is my favorite gene in platypus???)
apalazzo | October 31, 2006... when you finish your experiment at 5:15PM then exit the microscope room and discover that it's pitch dark outside.
apalazzo | October 27, 2006What type of biomedical research costs the most? That is an interesting question. With the NIH asking for a 20% cut in everyone's grant, our lab has been looking into who spends what, and where can we cut costs. An interesting number set fell out of this internal audit: how much each postdoc in the lab spends ... and there is an interesting trend.
We have basically 3 types of postdocs:
1) Structure biologists.
2) Biochemists.
3) Cell biologists.
So who do you think spends more money each month?
Structure Biologists. Between all the specialized detergents and many little consumables that they…
apalazzo | October 20, 2006Well I'm packing up to go off to western Connecticut for my fellowship retreat. Oh yeah, about that last minute experiment ... I nailed it! Not only did the experiment work but I also got the anticipated result confirming my pet theory.
Ain't that a pretty image of a cell! The cell was injected nuclearly (see inset) with XXXXX and the freakin' XXXXX not only got out but got targeted to the XXXXX. I'll tell you about the experiment some day, for now it's sensitive info.
As for Map that Campus, it'll be delayed until next week when I have more time.
Have a nice weekend.
apalazzo | October 17, 2006Sorry I'm not updating often. I've got a meeting this weekend and I'm trying to get that last piece of data (I know it sounds cliche, but face it, we all do it). What makes it worse is that my wife is out of town so now I have no excuse to come home at a decent hour. So instead of going on about RNA export or the joys of SDS-PAGE here's a little video brought to you by The Little Tetrad Swimming Achievers:
apalazzo | October 16, 2006It's not one of mine, waiting to be completed.
It's not from a competitor, scooping my precious results.
It doesn't even have much impact on my own work.
No it's a paper I once printed, and have heard about from others. It sits on my cluttered desk staring at me every day, and I just simply refuse to read it. Like an old rival we glimpse at each other every day, I pretend to ignore and it pretends to ignore me ... but the more I refuse to admit it's existence, the more it impose itself on my subconscious.
(and now with a Nobel given to the field ... this is obviously an important paper - if…
apalazzo | October 13, 2006Face it, they're unicellular ... they don't like groups (i.e. they are not urbanites). And even when they do grow together in a colony they have no real central control (like a brain) ... in other words they are anti government.
With their cell wall they are clearly isolationist. (I guess they're not neocons!)
They've shed many cellular functions ... such as nuclear envelope break down, microtubule based vesicular transport, centrosomes and most introns ... they are clearly not progressives. Note that these cellular characteristics were retained in more distant relatives of ours and thus it…
apalazzo | October 5, 2006OK now that the Science Nobels have been distributed it's time for the real awards to begin, the Ig Nobels.
How big is the Ig Nobel? It's janitor won last year's Nobel for Physics!
If you're in the Boston area, good luck getting tickets. If you can't get tickets or if you're outside the Boston area, you can watch the webcast, beginning tonight at 7:15PM. As for me, I was planning to attend, but when I woke up this morning I found myself in Montreal. If I can get away from all the food and drinking that comes along a visit to my big Italian family (or as they call themselves, "the clan")…
apalazzo | October 3, 2006Here is the annual list from The Scientist. (Click here for the article.)
The top 15 US academic institutions are:
1. St. Jude Children's Research Hospital, Memphis, TN
2. The J. David Gladstone Institutes, San Francisco, CA
3. Ohio State University, Columbus, OH
4. Vanderbilt University, Nashville, TN
5. Calvin College, Grand Rapids, MI
6. Trudeau Institute, Saranac Lake, NY
7. Michigan State University, East Lansing, MI
8. University of Florida, Gainesville, FL
9. Fox Chase Cancer Center, Philadelphia, PA
10. National Institutes of Health, Bethesda/Rockville, MD
11. Georgia Institute of…
apalazzo | October 3, 2006It's not as deranged as the last one. It must be for biotechs and pharma as "Get Promoted" and "Batch Released" do not really apply to this lab.
apalazzo | September 26, 2006(What follows was started at The Sunburnt Cow, an Australian Bar/Restaurant in Alphabet City - over a brunch that included unlimited Mimosas, Bloody Marys, Fosters and Vegemite.)
Here is the hypothetical situation:
It's the end of the world. You are barricaded in your lab. You have unlimited access to water. What lab supplies can you eat? What order should you consume them in?
A LIST OF POTENTIAL FOOD SOURCES IN THE LAB
(We realize that this depends on the model organism used in the lab ...)
- Yeast extract. Very rich. Probably very flavorful. This is a component of many broths used to grow…
apalazzo | September 19, 2006For those who don't know, John Yates is one of the most important mass spec (or "proteomics") guys out there (i.e. applying mass spectrometry to identify what protein you are analyzing). He developed tandem mass spec and is at the forefront of new technologies in this area. Yesterday he was in the Longwood area where he gave a seminar on the latest stuff coming out of his lab. The talk was OK, it would have been better if I was a mass spec guy as much of the talk was focused on the technology and how it has been used to probe biology ... rather than the biology itself. But I'd like to share…
apalazzo | September 18, 2006Well it looks like Stew has been souping-up his Science blog clearing warehouse, PostGenomic. A valuable source for searching the scientific blog-o-sphere (i.e. wasting time).
Interestingly there are stats for manuscripts floating round the blog-o-sphere and for many science blogs. Apparently The Daily Transcript is equivalent to Newsweek (does this mean that I'm the Fareed Zakaria of ScienceBlogs?)
For more on PostGenomic, visit Stew's blog Flags and Lollipops.
(Something really cool that I saw at Pg: HubMed, an alternative to PubMed. Click here to read the manuscript describing HubMed in…
apalazzo | September 18, 2006So Friday I posted a photo of an ad that went up in our lunchroom. The feedback was very indicative of the current mood of postdocs within the life sciences: frustration.
It all started with this ad:
And it sparked an interesting series of comments. The type of discussion that our profession needs. I'm not cheering for one side - but here are my two cents.
PIs, I understand, some of you look at this ad and you see passion, dedication and all these other virtues. And many postdocs (me included) see this ad as representative of an academic system gone amok. Sure we all value working hard and…