apalazzo | July 20, 2007Warning: the following may not be comprehensible for those not working in a lab.
So the other day, baymate and I were discussing how we use up our pipette tips. Not in terms of experimental procedures or in the types of orifices we jam them in, but in the order we remove our pipette tips from the pipette tip-box.
I tend to start off in one corner and work my way diagonally through to the other end:
In contrast my baymate likes to cut right through the middle of the box to form a horse-shoe pattern. (Quite a bold strategy)
In order to investigate this further we went around the lab and asked…
apalazzo | July 20, 2007 Corie sent me the info on Nature Network Boston's second pub night:
We are all about connecting scientists in the Boston area, both on the Web and in person.
The drinks night will be next Wednesday, July 25, 2007 at 6:00pm at the Mission Bar and Grill (http://www.themissionbar.com/index.html) located at 724 Huntington Avenue, Boston. It's on the Green E line, right by the Longwood medical area.
Come meet fellow scientists, other members of the NNB community (including some of our bloggers) and people from Nature's Boston office, in a very informal setting over drinks!
The first 20 or so…
apalazzo | July 19, 2007OK, lots of people claim that they understand what it is like to be in science and why so few Americans are in science. What is interesting is that all those that turned down a career in science (see the comments after this post) point out the reason why - lack of job security. But no, that can't be it (say the rest who don't have a clue), apparently scientist do it for the love of discovery. Others claim that scientists have to embrace industry. While it is true that industry is frowned upon in some circles, it's not that bad. Others who are obviously not in a tight situation and are perhaps…
apalazzo | July 18, 2007Yesterday's lab meeting went fine. Afterwards I got a chance to flip through some journals that I've ignored for the past 2-3 weeks. Among other items, I came across a commentary by Mike Rossner and Ira Mellman, the two big guys at the Journal of Cell Biology. The commentary concerns the resolution of a year long fight between the Howard Hughes Medical Institute and Elsevier. To force the hand of the publishers and to support open access, HHMI instituted a new policy - they would evaluate prospective and continuing HHMI investigators based on published manuscripts that were freely accessible…
apalazzo | July 16, 2007I've been busy preparing for a lab meeting - I'm presenting tomorrow. These last few months have been weird - since I've submitted my paper, about 1+1/2 months ago, I've been testing various theories, and toying with some ideas. Recently I knocked down two related proteins using siRNAs. Unexpectedly this treatment resulted in a striking morphological change. The knockdown cells don't appear to be dying, and their doubling rate is only slightly altered as compared to control cells but they now have all these micro-blebs.
Bellow the fold are two pictures, the first being the knockdown cells,…
apalazzo | July 12, 2007From our last trip but taken by Michael.
(A photo of the jazz group Nomo)
Here are some other concert photos:
Here are some random items and signs at the jazzfest venue:
This photo says it all:
apalazzo | July 12, 2007A couple of days ago I had a nice conversation with Mitch Waldrop who suggested that I check out a book by Jean-Claude Guedon entitled In Oldenburg's Long Shadow: Librarians, Research Scientists, Publishers, and the Control of Scientific Publishing.
This analysis of the history and future of scientific publishing has some very interesting factoids in it. I've only gone 1/5th through the book, but from the bit that I've read I can tell you that Guedon does not like the publishing industry and their aristocratic precedents. Also I find that the view of scientists is a little skewed, here is an…
apalazzo | July 12, 2007
(Fresh water rotifer feeding among debris (200x). First prize 2001, Harold Taylor - Kensworth, UK)
Now in it's 34th year, this microscopy competition is one of the most popular around. This year the general public is invited to vote for the winner. Click here for more details.
apalazzo | July 10, 2007First off, I will be hosting the next Postdoc carnival (What's up postdoc?) here on July 23rd. Email me your favorite blog entry on postdoc life.
Next up is a link that I missed in my science publishing linkfest: Revere mouthing off about open-access. One point that he makes has to do with PubMed:
It is currently NIH policy -- policy fought bitterly and with some success by lobbyists for big scientific publishers -- that NIH funded research be deposited in the publicly accessible online repository, PubMed Central, within 12 months of publication or earlier. Few scientists do it, and I'd guess…
apalazzo | July 9, 2007We spent the weekend up in Montreal where we caught some of the many shows at the Jazz Fest. If you've never been, here's what you're missing:
That's Marsh Dondurma from Israel - a friend of ours has a cousin in the band. Below the fold, I posted a couple of other clips from that same set.
Another band worth mentioning to you is Nomo. I wasn't able to record 'em due to the lack of memory in my camera and the level of alcohol in my blood - here's a vid from Youtube:
And you might be wondering, what type of person goes to the Montreal Jazzfest? Here's some examples:
As the day turn to…
apalazzo | July 6, 2007If you haven't heard, on July 2nd the U.S. Citizenship and Immigration Services agency placed a hold on visas for highly skilled foreign workers. Yes the US government is so crippled, it can't even manage to process the paper work for foreigners it wants to keep in the country. Over lunch I learned that the government maxed out its quota for this year. Why did the government let this happen? I thought that they needed highly skilled foreigners. Link to the USCIS press-room. Link to the press release.
The state of affairs is so bad, Microsoft is planning to open a software development center…
apalazzo | July 5, 2007Last week I posted an entry on Nature Publish Group, scientific publishing and web2.0. I'd like to add a couple of points, and throw out some links.
I would like to emphasize two points:
1) Feasibility. Yes we all want open information, but how to do it? And how to make it financially feasible? Publishing fees? Support from the NIH and other governmental assistance? Web based advertising?
2) Organization. Do we just dump everything on the web? Will this anarchy be great or will important research that is not directly relevant to your interests be lost? The web has been great to open up…
apalazzo | July 4, 2007I finally read the huge Nature paper that everyone has been talking about, the ENCODE project, or the encyclopedia of DNA Elements. ENCODE is a large scale concerted effort whose goal is to understand how the genome is used, maintained and conserved. In other words, what parts of the genome get translated transcribed into RNA, what do all these transcripts codes for, where are all the transcriptional start sites, what parts control gene expression (RNA production), how are histone modifications distributed across the genome, how are various DNA binding proteins distributed across the genome,…
apalazzo | July 3, 2007After the last miRNA post, I was alerted to this paper that appeared in the June 15th edition of Nature:
Thimmaiah P. Chendrimada, Kenneth J. Finn, Xinjun Ji, David Baillat, Richard I. Gregory, Stephen A. Liebhaber, Amy E. Pasquinelli & Ramin Shiekhattar
MicroRNA silencing through RISC recruitment of eIF6
Nature (07) 447:823-828
How did I miss that? The basic story is that eIF6 was co-purified with the RISC complex. To remind you RISC is a protein agglomerate that helps miRNAs downregulate the translation of targeted mRNAs into protein. And eIF6 is not a typical eukaryotic translation…
apalazzo | July 1, 2007I'm out of the lab and planning to enjoy the rest of the afternoon...
(thanks BTM)
apalazzo | June 29, 2007Yes, a new home for the NERD club. I just finished it last night:
http://www.newenglandrna.org/
Any suggestions?
apalazzo | June 29, 2007Although I do not own a television set, my wife and I watch the Daily Show and the Colbert Report every night, online. A couple of days ago Colbert had Daniel Gilbert on. Gilbert is a professor of Psychology at the Harvard main campus and has recently written a great book, Stumbling on Happiness. I had met Gilbert last year at a Seed dinner and saw him speak at an Edge/Seed sponsored round-table. His studies into happiness and affective forecasting are very insightful. To read previous posts on this subject click here, here, here and here.
(The clip from the Colbert Report is bellow the fold…
apalazzo | June 28, 2007Last night was nice. I dragged some buddies to Tavern at Central to hang out with the folks at NatureNetworks Boston. There we chatted with a few bloggers and some of the individuals responsible for NatureNetworks Boston (like Corie Lok.)
One interesting tid bit I'd like to share with you - I had a nice conversation with Kathrine (didn't catch her last name) who helps maintain the NatureNetworks site. We talked about recent successes and failures of scientific publishers and web2.0. Right now scientific publishing is in a state of flux, it is not clear how science communication will be…
apalazzo | June 27, 2007I just read in Corie's blog that Nature's new online local community (NatureNetwork Boston) is having a pub night.
I'll try to be there. Click here for details.
apalazzo | June 27, 2007Whiteboards are a staple of scientific laboratories ... often they are filled with ideas, diagrams, models and plenty of arrows. But they often contain doodles and other creative white noise generated by our active and restless brains.
In that vain vein, here's a clip that has been circulating in Youtube for a while: