apalazzo | May 6, 2006OK now time for some real blogging (I.e. rant).
Things I hate about journal publications.
1) Supplementary Data. You see a neat paper, you downloaded of the website and then as you go through the text you bump into "see supplementary data". Now I don't really mind this, however I hate that journals do not append the data to the end of the pdf file. Now I understand not everyone wants the hard copy of 2345 two hybrid reactions, but for most cases the 2 or 3 supplemental figures are crucial. It drives me mad. I get a paper emailed to me and half the data is missing! What is worse is if the…
apalazzo | May 5, 2006After coming back from a vacation, how many days does it take you before you can work? It seems like I can't even blog.
So instead here are some photos from my last trip...
apalazzo | May 4, 2006From a peice in the latest issue of Nature:
But this year, as three years of flat budgets begin to bite, Zerhouni's tenure at the NIH is being openly attacked by some scientists. The focus of their ire is his 'Roadmap', a set of activities that run across different NIH institutes and attempt to implement Zerhouni's vision for the agency. The critics say that the Roadmap isn't working and is diverting resources and attention from basic scientific research.
As the article states, it's hard to become the head of the NIH after such a rapid financial expansion. Harold Varmus was a tough act to…
apalazzo | May 3, 2006I guess that's why I study it. I usually never take these dumb online quiz things but provoked by another science blogger's entry I did this one anyway ... and yes I'm the ER.
You scored 46 Industriousness, 48 Centrality, and 7 Causticity!
You're the Endoplasmic reticulum! The ER modifies proteins, makes macromolecules, and transfers substances throughout the cell. It has its own membrane, and translation of mRNA happens within it. You tend to have two sides to you - sort of a jekyll and Hyde kind of story. One side of you tends to be rough and tumble, but also very useful. Your other side…
apalazzo | May 3, 2006OK I'm back from the west coast where we visited friends, family and the desert. My laptop has been resurrected and NO MORE RERUNS, I promise. Also I've seen that trackback spam has evolved (well perhaps intelligently evolved is closer to the truth).
Northern California was great (although in the past few weeks a bit wet). If I had sum up southern California in a word it would be "car", but in reality L.A. is quite elusive and massive. After parading around LA for a couple of days we saw a great documentary at the Egyptian, called L.A. Plays Itself. It's a tad on the long side, but for…
apalazzo | May 2, 2006(OK folks I'll be back this afternoon, this post is the last in serries of entries from my old blogs ... and this one is a hard core science entry from about 1 year ago ... enjoy)
Late last week I posted an entry on tubulin modification ... an area of research that one well respected cytoskeletal researcher described as "a cottage industry based on antibodies" ... Due to increased interest in the field, I'll recount here the tale of how tubulin modifications were first discovered.
In 1973 group of researchers (a team from Argentina!) decided to test whether proteins were repaired in neurons…
apalazzo | May 1, 2006(from my old blog)
Two days ago I was talking to a rotation student in the lab about the Nobel laureate and Columbia Professor Richard Axel, then last night at another BBQ (this time at Ben's place), the biology of olfactory was brought up, and finally this morning flipping through the Columbia University Magazine, there was an article on ... Richard Axel.
My first recollection of Dr. Axel was in a graduate student class I attended at Columbia. A bald, tall, and lanky individual in a suit walked into the room, sat down on the front desk, crossed his legs and said "So what do you want me to…
apalazzo | April 30, 2006(I'm still on my little trip - but I'll be back soon. Here's what I wrote when I came back from Spain last summer)
Is this entry about the eventual fall of the west?
Perhaps not directly.
Although wedding plans loom large, the people and places from our last trip to Iberia keep coming back to haunt me.
No this entry is about the demise of the Andalus Caliphate. From an article in today's NY times about Medina Azahara, the summer home of the Andalus Caliphate, whose capital was in the nearby Cordoba:
Medina Azahara, also known as Madinat al-Zahra, was an Islamic metropolis built in the 10th…
apalazzo | April 29, 2006(here is a nice post from my old blog back in early December '05 - one of the least scientific ones you'll get from me)
While my column is washing, and my brain is fried, I should finally write this entry ...
A while back, right around the time of Katrina, I read a spectacular book, The Control of Nature by John McAfee (Amazon site).
When man's interests conflict with an ever changing environment, what does man do? He/she fights change.
(All images were hijacked from maps.google.com.)
Part 1
The Army Corps of Engineers vs the Mississippi River.
As time goes on rivers carry sediment from…
apalazzo | April 28, 2006(two entries from my old blog)
I've been reading Ernst Mayr's This Is Biology: The Science of the Living World. In it there is this great quote:
It is often asked why we do science? Or, what is science good for? ... The insatiable curiosity of human beings, and the desire for a better understanding of the world they live in, is the primary reason for an interest in science by most scientists. It is based on the conviction that none of the philosophical or purely ideological theories of the world can compete in the long run with the understanding of the world produced by science.
(second…
apalazzo | April 27, 2006(from my old blog)
Every subject has its lingo and its share of strange terms. Add abbreviations and acronyms, and certain areas of expertise can be almost incomprehensible. Then there is Biology.
Life has a diversification machine, evolution. Thus those who study life (i.e. Biologists) have lots of proteins and genes to name and to investigate. Humans have about 23,000 to 30,000 conventional genes, and many other non-conventional genetic elements such as small RNAs. On top of that these same 23,000+ genes are also found in other vertebrates and many are found in almost every eukaryotic cell…
apalazzo | April 26, 2006(This entry was from 12/22/05 thus the Xmas reference)
Well here I am in rainy Seattle visiting the inlaws. Last night we prepared artichokes for dinner. Naturally the conversation turned to how the consumption of artichoke has a curious effect on the sense of taste: everything tastes sweet even water. If you've never experienced this before it's because you've never had fresh artichoke. Pickled artichoke hearts don't have this property.
So entering "Artichokes and Sweet Taste" into Pubmed what do you get?
Bartoshuk LM, Lee CH, Scarpellino R, Sweet taste of water induced by artichoke (Cynara…
apalazzo | April 25, 2006(Just to remind you all - I'm away on holiday and I've pre-scheduled the publication of several posts from my old blog at blogspot. This next entry was one that I got a lot of 'tsks, tsks" for - it was intrended tio be a tad toungue & cheek. Incidentally the values of the various h-indexes listed here must have gone up.)
About a month ago I had a conversation with my thesis advisor about the h-index. It is a new method, proposed by Jorge E. Hirsch of UCSD to quantitatively measure a scientist's influence. His proposal was published in PNAS and Nature had a little report on it. Here's a…
apalazzo | April 24, 2006(from my old blog)
OK here's a post geared mostly to cell biologists. My big pet peeve about reading the scientific literature is ... colored fluorescent images.
Why do people insist on pseudo-coloring their images? I know that you want pretty pictures and as every kid knows the more colorful the picture the more adoration one gets from approving parents ... but we're talking about data and instructing/convincing your fellow peers about new findings.
So why is color bad for data presentation?
Your eyes are better at detecting various shades of grey than shades of any hue. Or to rephrase, it'…
apalazzo | April 23, 2006(from my old blog)
OK this week I've been obsessed with the endoplasmic reticulum (ER). This organelle is comprised of a continuous network of membranous tubes (and sheets) that extends to the cell periphery. In addition ER sheets also envelopes the nucleus - forming a bilayered nuclear envelope with an outer nuclear membrane and inner nuclear membrane.
The extended part of the ER though is mostly tubular, as I displayed in an earlier post on Immunofluorescence images:
So the question becomes ... how do you form tubular organelles?
Well Gia Voeltz, from our lab just published a paper in…
apalazzo | April 23, 2006Non-cell biologists have often viewed the cell as a bag of molecules. Over the years as cell-biology has developed, it became clear that this was a simplistic generalization. Cells are organized by a dynamic cytoskeletal network that can organize the cellular architecture. Cells are also subdivided into membrane bound organelles. The deeper we look into the cell the more we find that each cellular component is subdivided into specialized regions.
Now it would seem that organelles themselves are subdivided. As all good cell biologists know, the endoplasmic reticulum (ER) is a large continuous…
apalazzo | April 22, 2006(from my old blog)
Portuguese (tissue) culture:
Looks like she's mouth pipetting, or drinking (we're not sure) some yummy tissue culture media. I hope that this newspaper clipping won't spark riots.
apalazzo | April 21, 2006(from my old blog)
Just read an article in the last issue of JCB, where the authors used a nifty new technique to investigate when and where certain RNA binding factors associate together.
What's neat, is that this technique, bimolecular fluorescence complementation (or BiFC) works by fusing each half of a fluorescent protein (in this case yellow-fluorescent protein; YFP) to two proteins of interest (in this paper the RNA export factor TAP/NXF1 and the RNA binding factor Y14). To regenerate the intact YFP molecule the two proteins in question must come together. Since the fluorescence can be…
apalazzo | April 20, 2006So it looks like ... my laptop dying + rejected paper + a resubmitted paper = vacation to the west coast.
Does this mean that you'll be stuck reading about how cephalopods perform really cool tricks (from the CBC, not some other blog)?
Fear not!
In the next week and a half, some posts from the old blog will appear here so that you'll all have something to read while I'm gone. It's a Transcriptional retrospective!
Enjoy.
apalazzo | April 19, 2006A new paper out in Nature, brakes through the diffraction barrier to see things that have never been seen before. Using this novel fluorescence-microscopy technique called STED (stimulated emission depletion), Willig et al., see Kiss and Run. And yes they see it!
OK ... I know, you have 2 questions. How does STED work? and What is Kiss and Run?
Rayleigh's law of resolution maxima, which says that you can never resolve two dots that are closer together than the ~size of the wave-length of light used to probe the sample, defines how small we microscopists can see in the two dimensional plain of…