apalazzo | August 9, 2006I got this funny/cynical email from a good friend. What do you think?
In the jungle of research, a small white rabbit stumbles upon a wolf.
"What's a bunny doing here? " says the famished wolf.
"I am doing an important piece of research work for my thesis, " says the rabbit.
"And what is that?"
"It's all about the superiority of rabbits on wolves."
"Hin hin."
"Don't you believe me? Come in my place."
And no one ever heard about the wolf anymore.
Sometimes after that the rabbit meets a Tiger in the jungle of research.
Asked what he is doing in such a perilous place, the rabbit says: "A thesis…
apalazzo | August 8, 2006There is a paper in last week's Science that describes a proofreading mechanism in prokaryotic (i.e. bacterial) RNA Polymerase, the enzyme responsible for transcribing DNA into RNA. When RNA Pol incorporates the wrong base into a growing RNA, the enzyme moves two steps back and cleaves the dinucleotide fragment (the mismatched DNA-RNA base pair plus the preceding pair DNA-RNA pair).
So far that's OK. RNA Pol can correct mistakes and thus can transcribe with increased fidelity etc. But the cool part is that the data from this paper supports a model where the mismatched nucleotide participates…
apalazzo | August 8, 2006A paper from a week or so, describes a method for detecting regions in the genome where DNA wrapping takes place. So what (you may asked) is DNA wrapped around?
Nucleosomes!
Each nucleosome (red balls in the cartoon) contains 8 histone proteins (two each of Histone 2A, 2B, 3 and 4). In addition, histone 1 (yellow in the diagram) hangs out at the periphery and is involved in linking neighboring nucleosomes together (we think). Histones are not only the most conserved eukaryotic proteins but also the most abundant. In fact, if you were to run a protein gel and stain for total proteins (by…
apalazzo | August 7, 2006I haven't done this in a while:
Below the fold you'll find links to an interview with Alan Parker editor of Nature Genetics, Boltzmann and entropy, Big Biology, Tanzanian society (as seen through a medstudent from the west) and a note on affirmative action.
Hsien Hsien Lei of Genetics and Health interviews Alan Parker, editor of Nature Genetics. Here's an excerpt (re:open access):
As for Nature, my guess is that it will remain a 'reader pays' journal for the foreseeable future. The primary reason is that it costs a great deal of money to produce. One thing that may not be apparent from the…
apalazzo | August 6, 2006What a nice day. Sitting on the esplanade, reading Colin McGinn's The Making of a Philosopher (a personal memoir + thoughts on 20th century philosophy). And I come across this:
Nowadays psychology has pretty much the shape that Chomsky advocated, and it is hard to remember the time when behaviorism was the prevailing orthodoxy. I still think this provides a valuable lesson in questioning orthodoxies that go out of their way to deny obvious facts -- as behaviorism in effect denied that we have minds. The sure mark of an ideology, in science and philosophy as in politics, is the denying of…
apalazzo | August 5, 2006You can find almost anything on Youtube.
Here is a video from Nikon (maker of great microscopes) of mouse fibroblasts (connective tissue cells) dividing and migrating around a coverslip.
Ah, this is why I became a cell biologist. Look at those guys go! (And to think that some would call them bags of molecules -which they are ... but they are pure beauty) Also notice that the cells must contract and round up just before they divide.
While you're at it visit Nikon U. a web resource for microscopy.
apalazzo | August 5, 2006Well two weeks ago in Science, two reports came out about yet another species of small RNA ... rasiRNA ... uhm ... piRNA (OK they haven't harmonized their nomenclature yet).
So here is a brief review of the types of RNA:
- mRNA (messenger RNA). These are the RNAs that encode polypeptide chains.
- rRNA (ribosomal RNA). These form the core structure of the ribosome. The ribosome is the enzyme that translates the tri-nucleotides, to amino acids. In this way it synthesizes (or "translates") proteins from mRNAs.
- tRNAs (transfer RNA). These are used by the ribosome to translate the tri-nucleotie…
apalazzo | August 4, 2006My baymate and I started a little discussion about lab fashion. Why? Well I'm a pretty ardent wearer of sandals, I'll wear them until late fall if I have to. I'll wear them with jeans too. But under no circumstances will I wear sandals with socks.
We then listed all the faculty who combine these clothing items on a regular basis (sorry, the list is confidential).
This brings me to my question to all you out there is: why wear sandals with socks? (And why does the sandals with socks phenotype correlate with being in research?)
Now while we were on the topic we asked a deeper, in some sense…
apalazzo | August 4, 2006OK here is this weeks aerial photo:
Click here for a larger version
and the hint:
Where we came from
(But our cousin was found in a cardboard box)
As usual leave your guesses in the comment section (or if you don't want to ruin it for others email me, I'll post emailed answers over the weekend) .
apalazzo | August 3, 2006Another "We support the postdocs" editorial at Nature Cell Biology:
The days when one could imagine starting a laboratory following a short postdoctoral position, or even with no postdoctoral training at all, are long gone. Nowadays, extensive postdoctoral training is essential not only if you are pursuing an academic career, but also for a research career in industry or biotechnology.
Although the pool of postdocs has expanded significantly in the past two decades, an increase in the number of academic positions, and other research opportunities that they can subsequently move to, has not…
apalazzo | August 3, 2006With everything going on in the world (polticaly, environmentally and otherwise), you would think that the US government would pump money into developing technology that allows for cheaper, cleaner, more reliable, more sustainable sources of energy. These technologies would not only allow us to prosper (lots of cheep energy = increased productivity), but also to decrease our dependence on middle east oil (for obvious reasons).
So com'on folks! Lets build nuclear power plants, fund research into fusion power, or at the very least try to make our current energy usage more efficient.
But if the…
apalazzo | August 2, 2006As I've written before, things are happening in California. I also learned that postdocs at University of Connecticut Healthcare Center (UCHC) joined (formed?) a union, University Health Professionals (UHP), in 2004. From the PRO/UAW site (PRO=Postdoctoral Researchers Organize):
A recent article in Science's Next Wave outlines many of the improvements won by unionized Postdocs at the University of Connecticut Healthcare Center (UCHC) though collective bargaining. In the first contract, Postdocs won significant wage increases--as much as $10,000 in some cases, annual cost of living…
apalazzo | August 2, 2006Heatwave = sitting inside a dark room and doing some work. It's funny I'm laptopless, and my life still revolves around computers (this one is attached to my microscope). Since I haven't been keeping up with the latest, all I have to show you are some nice pics of Endoplasmic Reticulum (ER). Enjoy:
Here's a closer shot (different cell):
Here is just a picture of fluorescent protein in a hepathocyte (kidney cell). Note the negative stain (absence of fluorescence) labels some organelles and some filaments:
And last, here is a cell expressing a fluorescent ER marker, but the poor cell just…
apalazzo | August 2, 2006... so hot that the cable on my laptop's AC adapter MELTED. (If any of you is expecting an email from me - this would explain the delay.)
Last night I was typing a summary of the recent rasiRNA/piRNA papers (while playing scorched3D) when my computer switches to battery mode. At that point my wife asks me "do you smell burning plastic?"
(Maybe I can blame that on scorched - a ridiculous game that my brother and I used to play about 15 years ago - little tanks lobing missiles at each other while uttering insults and bizarre quotes - "I love the smell of napalm in the morning". I guess some…
apalazzo | July 31, 2006Yes, things are on the move (since we last checked) in California.
Get more info here.
(Yes I'm a month behind - but someone just told me about it ...)Nope, they filed 7/25/2006.
apalazzo | July 30, 2006... or how the human brain is wired. Beware we'll be hearing from David Brooks, Frank Rich, William Gibson (Thomas Kuhn), and a preview of a Noam Chomsky and Robert Trivers discussion.
So I'm reading David Brooks in today's NYTimes, and it's the same old thing ... he's trapped in a different universe it seems. Apparently America (and Israel) are all powerful. They can do anything and whatever they want:
Lebanon is a chance to show that the death cult is not invincible.
To its enormous credit, the Bush administration has kept its focus on that core reality, and it has developed a strategy…
apalazzo | July 30, 2006Yes I've been doing some hardcore science blogging. But apparently my blog is
not just about science, but art, food, music, citylife and other mental stimuli.
And so enjoy.
PS I just got the album - it's getting better with every listen.
apalazzo | July 29, 2006Thursday marked the 350th anniversary of Spinoza's excommunication.
Here are some exerpts from a great OpEd by Rebecca Newberger Goldstein in today's NYTimes:
The exact reasons for the excommunication of the 23-year-old Spinoza remain murky, but the reasons he came to be vilified throughout all of Europe are not. Spinoza argued that no group or religion could rightly claim infallible knowledge of the Creator's partiality to its beliefs and ways.
...
Spinoza's reaction to the religious intolerance he saw around him was to try to think his way out of all sectarian thinking. He understood the…
apalazzo | July 28, 2006Yes this is the surprising result interpretation of Jonathan Weissman's paper in Science. For non cell biologists, click here first, to get some background on the unfolded protein response (UPR) and ER associated degradation (ERAD). And to learn about some recent developments on ERAD, click here.
OK on to the HARDCORE cell biology ...
Remember under UPR conditions cells want to stop translating ER targeted proteins and instead synthesize chaperones and ERAD components. UPR inhibits translation through PERK (see the post on UPR) but what happens to the mRNA that encodes ER targeted proteins?…
apalazzo | July 28, 2006In the August issue of The Scientist, there is an article entitle "The Inequity of Science" (Not online yet). It describes how the top academic institutions are getting more and more of the total NIH funding.
Between 1994 and 2004, in the rankings of universities and colleges according tototal R&D expenditures in biological sciences, the difference between the number one school and the 100th school more than doubled.
Echoing Bob Weinberg's commentary,
In 2005, the principal investigator on the biggest grant, Eric Lander at MIT, received more than $50 million, nearly seven times the…