apalazzo | April 6, 2006Surfing on William Gibson's blog, I stumbled on to this amazing video of an amphibious snake-like robot.
apalazzo | April 5, 2006then you read this story: Prof denied grant over evolution. Agency wants proof Darwin is correct; But McGill says committee's reasoning is faulty. From the Montreal Gazette:
McGill University says the Social Sciences and Humanities Research Council made a "factual error" when it denied Professor Brian Alters a $40,000 grant on the grounds that he'd failed to provide the panel with ample evidence that Charles Darwin's theory of evolution is correct.
Now I don't like writing about ID, because it's honestly it's like talking about individuals who don't believe in algebra, but I just can't…
apalazzo | April 5, 2006Last night I was invited to a Seed dinner in Cambridge. The idea, I guess, was to throw together scientists from various disciplines and Seed contributors, and observe the resulting chemical reaction.
I had very interesting discussions with Drew Endy of MIT who is developing a molecular tool kit to engineer prokaryotes. Engineer? Well the idea is to reprogram bacteria to perform simple tasks such as turning on and off the production of fluorescent proteins over a regular time interval. These blinking bacteria are just the tip of the iceberg. Endy and others (such as Pam Silver) want to have…
apalazzo | April 4, 2006Plagued with scandals and other baggage, today DeLay announced that he's giving up.
Usually I've steered clear of pure political talk on my blog, although those of you who know me personally know that I've been politically active. Well with DeLay's announcement I have a story to tell - and it's connected to science, or to be precise NIH funding.
Back during the "Contract with America" years the NIH was in desperate need of funding. The Republicans, in full starve the beast mode, campaigned to slash government spending on frivolous spending items such as Government sponsored research. Numerous…
apalazzo | April 4, 2006
No this is not an entry on shmooing, but on practical tips on working with Saccharomyces cerevisiae.
(OK confession, I have worked on yeast briefly as a rotating student in Liza Pon's Lab at Columbia.)
Much of modern cell biology is based on Yeast genetic screens, the most famous are those performed by Leland H. Hartwell and Paul Nurse to determine genes necessary for cells to divide properly (the CDC, or cell division cycle, mutants).
The only tip I can give you is to pay attention to what is done in yeast, the rule of thumb is that the yeast field is 1-2 years ahead of the rest.
That…
apalazzo | April 3, 2006I'm not sure about the history of "the three types of experiments" (3tes), 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 instead of A, B and C. I have a few comments about the…
apalazzo | April 2, 2006(from the archives)
As a microscopist you are often are stunned by the beauty of what's on your microscope slide. I remember as a grad student showing this technician (a former doctor from China) a slide where cells were stained by immunofluorescence against microtubules. After peering into the microscope he turned to me and said, "there must be a God". Uhm ... yes quite beautiful stuff.
So it came as no surprise when a good friend of mine sent me a link to A Slice of Life Scarves. This company uses motifs from the life sciences as patterns for their scarves and ties. Besides Golgi scarves (…
apalazzo | April 1, 2006A major field of research in the "RNA field" is the quality control of mRNA production.
Remember from the central dogma:
DNA=>RNA=>Protein
When "genes are activated", what is really going on is that a DNA segment (i.e. the gene) is copied into RNA, that is then processed to form messenger RNA (mRNA) in the nucleus. During this processing, RNA acquires several modifications: a Cap is added to the front end (5' end), a poly-A tail is added to the back end (3' end), and any non-coding regions are spliced out of the middle. The mRNA is then exported from the nucleus into the cytoplasm where…
apalazzo | March 31, 2006I just couldn't believe it ... read the confession here.
Yeah I know ... crazy. But now that I have your attention, click here to contact your house representative to tell him/her to support the NIH by increasing funding in the new House budget resolution.
What is the NIH? ... the National Institute of Health is the most important source of funding for basic research in the biomedical sciences.
From capwiz:
Last week the Senate passed its FY 2006 Labor-HHS-Education appropriations bill (H.R. 3010) with a total of $29.415 billion for NIH, a 3.7 increase over last year. In June the House…
apalazzo | March 31, 2006Weird things are afoot.
It all started last time the crazies got together. We had our fill of food and drink. The conversation had turned to nudist beaches and the next thing we knew, books were stolen, a member was held up, and then German Nihilists hijacked the Boston bookclub blog.
That's when we thought "What the hell is going on?"
Then a couple of days later this picture appeared:
Was our finger-gun-wielding-German-nihilist book thief toying with us? From the picture we deduced that he/she/they was obviously a scientist, perhaps a molecular biologist?
Staring closely at the picture of…
apalazzo | March 31, 2006So a couple of weeks ago, I wrote an entry about gender and science. I encourage you not only to read the post but also the comments. In that post I mentioned a 2003 Caltech postdoc survey that parsed some of the data by gender. Again I strongly recommend that you examine the raw data.
Here are some interesting differences between Female and Male Postdocs from this 2003 survey:
- Male postdocs are more likely to have children.
- Male postdocs with children have their wives take care of the kids, female postdocs with children rely more on daycare. As a result, female postdocs spend more on…
apalazzo | March 31, 2006Harvard announced yesterday that it would waive tuitions for undergrads whose families earn less than $60,000 annually. From the Harvard Crimson:
The newly expanded financial aid program, which will also reduce the contributions of families with annual incomes between $60,000 and $80,000, is expected to cover more than 1,500 students--nearly a quarter of the College--in the next academic year, Dean of Admissions and Financial Aid William R. Fitzsimmons '67 and Vice President for Administration Sally Zeckhauser said in a joint interview this evening.
With the announcement, Harvard jumps to…
apalazzo | March 30, 2006If you haven't, go and read to evolgen's entries on the Specter-Harkin Amendment that successfuly passed in the Senate to increase the NIH budget. Next up is the House. If you care about basic research in the biomedical sciences contact your local reps pronto.
Contact Your US Representative about the NIH Budget (@ evolgen)
The First Step in Increasing the NIH Budget (@ evolgen)
apalazzo | March 30, 2006Last night I was at another party in Cambridge, a good friend of mine is leaving Boston to go work for Pfizer in NYC. (Aside - why does it seem like anyone in Cambridge who is not a student or a professor, works for Biotech, Pharma or an IT start up?)
In any case I had an interesting conversation with XXXX who works for a Venture Capital Firm that specializes in funding new biotech startups. We got into an interesting conversation about the current status of the pharmaceutical industry in the US and overseas.
Apparently the pharmaceutical market is in a weird state. Venture Capitalists are…
apalazzo | March 29, 2006Remember that special moment when everything changed. Were you listening to a particular song? Or was it some food? Well a couple of friends just posted about such associations.
The first is from Tall Med Student, a former Harvard postdoc who is now a med student at the University of Calgary.
In his ode to Boston, he writes:
Korean food. Three places come to mind: Café Han River at St. Mary's, Korea House in Chinatown, and best of all, Buk Kyung II in Alston. At that last place, I was introduced to jajang myeon, which was spectacular there. Interestingly, one day while in Ä°stanbul last…
apalazzo | March 29, 2006OK after making fun of System Biologists out comes Peter Sorger's latest paper in Cell.
In this paper, Sorger's team collected almost 8000 intracellular measurements (they collected some of the data directly and got the rest from the literature - I'll have to check on that) plugged it into an algorithm or a ...
... compact representation of the entire compendium by using discriminant partial least squares regression (DPLSR; Janes et al., 2004). A DPLSR map was created such that the signaling proteins and cytokines were projected onto a set of "principal components" that maximized covariation…
apalazzo | March 28, 2006(from the archives)
Once upon a time, we made the necessary chemicals from scratch to purify DNA from bacterial cultures. These days, for a couple of dollars, you can get all the reagents you need all packaged in a nice box - these things are called commercial "kits".
You may ask, why do you use these kits - Is it laziness? or consistent results? A combination of these answers I guess. In the end those that never made the reagents from scratch are less likely to understand how the procedure worked, and how to trouble-shoot when the procedure fails. The latest kit (from Qiagen) had this flyer…
apalazzo | March 27, 2006The van Oijen lab (here at HMS) had a nice paper in Nature where they indirectly observe single T7 DNA polymerase complexes copying DNA.
How do they do it? One end of the DNA is fixed while the other side is coupled to a bead that can be visualized. A laminar flow is applied to the reaction causing the DNA strand to stretch out. Thus the bead becomes a marker for the length of the DNA.
As the T7 complex duplicates the leading strand, the uncopied lagging strand agglomerates. Since the lagging strand is fixed to the cover slip, the DNA shortens and this reels in the bead like a fish on a line…
apalazzo | March 27, 2006Want to be a Cell Biologist? Take a look at this phase image of a rat hepathocyte (liver cell) that I took sometime last year. Try to identify the three mystery organelles A through C
And to be totally clear:
A) The big blob in the lower right hand corner
B) The dark round organelles
C) The squiggles
Bonus question:
Which of these organelles contains DNA?
apalazzo | March 27, 2006Well after that mRNA song, I got wind that there is an x-ray crystallography poem floating out there. So we searched, and searched. Finally undercover agents from the Steitz lab emailed the sought-out credo to our contacts.
Allegedly, this poem was composed by Bernard Rupp, who teaches a famed crystallography course.
So without further ado, here it is:
This is my x-ray machine.
There are many like it, but this one is mine.
My x-ray machine is my best friend. It is my life.
I must master it as I must master my life.
Without me, my x-ray machine is useless.
Without my x-ray machine, I am…