apalazzo | October 10, 2007I'm in Italy. Until I get back I've set up my blog to repost some old entries. Here's a post from last year.
Yesterday, while driving up to Ipswich to spend the day at Crane beach and watch the see the annual July 3rd Fireworks, a group of us gabbed about the transient nature of being an academic.
Living from place to place, moving until you are in your late 30s, an academic is expected to travel and see the world. You live in various places; experience the day to day hustle of different cities, towns and often countries. You absorb the local customs, the ideas, the history. You attempt to…
apalazzo | October 8, 2007I'm in Italia. Here's one of my favorite entries. It first appeared last year.
You can clearly divide scientists into two categories, those who build new models and those who prove old models. The explorers and the crusaders. Usually the former are seeking the truth, or something close to it, while the latter are trying to confirm their own theories as if the idea was more important than reality.
As you can guess, I do not have a high regard for the latter group. Unfortunately there are a lot of crusaders around. In some way we all are part of this second group to some extent, but…
apalazzo | October 5, 2007I'm in Italy. Over the past two weeks I've been reposting my entries on technology. Here is a related post on Le Corbusier and his conception of the modern city.
Seed is disseminating questions to its bloggers (I guess a la www.edge.org) so this week the question is:
If you could cause one invention from the last hundred years never to have been made at all, which would it be, and why?
The invention I would choose to uninvent? I spent the weekend asking some friends. Some answers were machine guns, the atomic bomb, spam, cars ...
Cars did strike something deep in me. Along the lines of…
apalazzo | October 3, 2007Still in Italy. Here is a post from last year that was a follow-up to the entry that was reposted yesterday.
Lets think about technology for a moment. Here I am typing on this laptop. Ideas flow (misspelled and grammatically incorrect) from my brain to my fingers to the keyboard ... over a wireless network ... into the vast ethereal space (known as the internet) ... to your home/workplace/café.
So what good is any of it?
You exclaim ... that's preposterous. Technology is good.
You would then continue ... All these gadgets and gizmos, they're good on many fronts. They make us live longer,…
apalazzo | October 2, 2007I should be walking around the family olive grove by now. Here is yet another old post from last year.
OK here is a myth that I'd like to explode (or at least be provocative about). Technology is NOT inevitable.
Say what?
We humans think that technology increases steadily. With every space shuttle and iPod, humanity advances by one small step. Sort of like that image of the ape walking more and more upright
... yeah that one. But the steady progress of technology is a myth.
Then how does it advance? Punctuated equilibrium? Not really. Humans are adept at finding tricks and shortcuts. We'…
apalazzo | September 30, 2007Yes still in Italy. Looking back at this post, it looks like most of the small biologists (excluding structural biologists) who practiced the molecule-centric approach have been weeded out by the stagnation in NIH funding, but I still beleive that the temptation to perform such research is still there for many young scientists ... so here goes.
As time goes on my ability to cope with the rich experience of daily lab life requires me to rant every so often. So here is today's rant.
There are two approaches to small biology, studying molecules and studying processes. Stay away from the…
apalazzo | September 28, 2007Yes you've guessed it, I'm in Italy. Here is another entry dealing with scientific thinking.
Spurred on by some comments left by Coturnix on the Three Types of Experiments entry, and by the Microparadigm paper (see my entry, and another discussion of this paper at In the Pipeline), I now present to you ... the significance of negative data.
Now most of the older (and well read) philosophers of data such as Kuhn, Popper and Feyerabend were obsessed with the physical sciences, and as Ernst Mayr has pointed out in several books, they're ideas are less applicable to the life sciences. Even the…
apalazzo | September 26, 2007Still in Italy. Here's another old entry for you.
I'm not sure about the history of "the three types of experiments" (3 T's), but they are referred to quite often in the labs I've been in. So what exactly are they?
Here goes ...
Type A Experiment: every possible result is informative.
Type B Experiment: some possible results are informative, other results are uninformative.
Type C Experiment: every possible result is uninformative.
There is even a little saying that accompanies this ...
The goal is to maximize type A and minimize type C.
There are some that even name the 3tes 1 through 3…
apalazzo | September 25, 2007The Nobels are coming up. Here is last year's prediction (note that I had listed Mello and Fire).Who will win this year? You tell me.
Some guesses for the Medicine & Physiology (or perhaps Chemistry) below the fold. Warning - the predictions presented here are highly biased towards cellular physiology.
Membrane Traffic. James Rothman and Randy Schekman. Maybe you could throw in Peter Novak.
There's a rumour that intracellular signalling may win. Tony Hunter (phospho-tyrosine), Tony Pawson (protein signalling domains) and Allan Hall (small G-protein switches).
Structure of the first virus…
apalazzo | September 23, 2007Jenni and I spent the last 3 days in the big city, meeting friends, celebrating weddings and preparing to leave for the mother country.
We stayed with our good friend Jan who lives in Morning Side Heights near the Columbia main campus. Right outside his apartment the Cohen brothers were filming their latest flick "Read an Burn" (?) - all we can say is that Grant's Tomb was transformed into the Department of the Interior.
I wanted to tell you something about this incredible result about cells and left/right asymmetry (yes, I know that sounds strange but it's incredible), but we are leaving…
apalazzo | September 21, 2007I'm off to NYC and then Italy for a whopping 3 weeks. I'll be visiting my mother's hometown, my father's father's hometown and other sites along the Apennines. I may post little items while I'm gone, but until I'm back some old entries will be appearing on The Daily Transcript.
Ciao.
apalazzo | September 20, 2007One lobbyist's recommendations on how academic publishers should counter the open access movement. Do I need to write anything? Just read it here.
Also see
- Eric Dezenhall PR memo to publishers leaked (Coturnix)
- Publishers prepare for war over open access (Jim Giles, the New Scientist)
And previously:
- PRISM - a new lobby against open access
- The latest reactions to PRISM
apalazzo | September 20, 2007Unfortunately I'll be out of town, but if anyone is in the Boston area, I encourage you to attend. All the info is in this email I just got from Corie:
You've seen the website, now meet the people who are on it (and who run it). Nature Network Boston (http://network.nature.com/boston) is hosting the 4th of its monthly pub nights for Boston-area scientists next Tuesday, September 25 at 6pm. If you're new to NNB or haven't been able to make it to our previous events, this is your chance to get out of lab and meet scientists from that university across the river or that biotech company down the…
apalazzo | September 19, 2007From today's email:
Dear Colleague:
NIH is inviting health professionals engaged in biomedical and behavioral research to apply online for a loan repayment award. The loan repayment programs (LRPs) are a vital component of our nation's efforts to recruit and retain highly qualified professionals to careers in research.
NIH annually awards loan repayment contracts to approximately 1,600 health professionals with an average award of $52,000. More than 50% of the awards are made to individuals less than 5 years out of school. Approximately 40% of all new applicants are funded and 70% of…
apalazzo | September 19, 2007Well it would seem that in the past couple of years pop science has discovered RNA. Via Genomicron, I found this article in Scientific American from a few years back. Unfortunately all the lit on RNA in the popular press is a little overhyped and not very well understood.
Sure, there is probably a lot of non-coding RNA that does important work. Sure gene regulation through micro-RNAs is one of the biggest discoveries of the last decade. And yes the evolution of eukaryotes is intimately tied in with RNA splicing - the main purpose of the nucleus is to separate mRNA synthesis and processing…
apalazzo | September 18, 2007Over at The Scientist, they're asking
Tell us what your favorite life science blogs are and why by clicking the button and leaving a comment, and we will publish a list of the most popular choices across the different areas of life sciences. With your help we hope to provide a list of who is currently hot in the science blogosphere, and why you should be reading them.
Attila Csordas, who was asked to contribute to the main article chose ... me (amongst others). Several additional bloggers gave their 5 favorites.
So who are my favorites? I hate that idea - top 5 ... so instead I'll tell you…
apalazzo | September 18, 2007Let's face it, you are probably procrastinating right now.
I'll begin by stating that this post was inspired by Hsien-Hsien Lei's new facebook community.
Lets start off with a video on how to procrastinate:
One of the greatest effects of the Internet: procrastination. As we've advanced to web2.0, procrastinators now can produce junk as well as consume it. (Yes blogs too.) To read one blogger's daily procrastination routine, visit David Bradley's longish essay on How to get Nothing Done.
Want to cut down on procrastination, go read this website produced by California Polytechnic State…
apalazzo | September 17, 2007I've written much about the Nuclear Pore Complex (NPC). This large molecular gate controls the flow of molecules into and out of the nucleus. Recent work (see this post and this new paper) describes how filaments containing "FG repeats" form a matrix in the center of the pore that blocks the movement of large but not small particles. To cross the pore (the black blobs in the pic below), big macromolecules must associate with factors (or nuclear transport receptors, NTRs - red blobs) that can melt and become part of the matrix (the squiggly spaghetti strings).
From a top-down view, the NPC…
apalazzo | September 15, 2007One of the most watched cell biology videos of all time. A neutrophil uses chemotaxis to chase a bacterium around a field of red blood cells. Notice how the neutrophil can suddenly change direction. This clip was shot over 50 years ago by David Rogers at Vanderbilt University.
apalazzo | September 13, 2007Me: So how long has it been since you first submitted your paper to XXX?Resident Genius Postdoc: Next week it'll be eight months.Me: Wow, that's almost like pregnancy.Resident Genius Postdoc: At least there's an end to pregnancy.Me: Yeah, I guess you can always get a c-section.
Question: why don't journals have some policy about how long they can hold a manuscript that is up for review? Journals should promise to review any submitted manuscript within a certain number of days. If the review process (including the first and second review periods, but excluding the time it took the authors to…