apalazzo | April 6, 2007I have no time to blog today (and no time for Map that Campus - next week I'll have a new Northwestern mystery campus for ya).
Here's an entry from 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…
apalazzo | April 4, 2007Apparently Reed Elsevier, publisher of countless academic journals such as Cell, Neuron, Current Biology and the Lancet, is also organizing arms exhibition shows.
In a bizarre development, the editors of the Lancet agreed with researchers who want to start a boycott of their journal.
To read more:
The Lancet's terrible dilemma (Effective Measure)
Should Elsevier journals be boycotted? (Evolving Thoughts)
MDs, Scientists Call For Elsevier Group Boycott (Living the Scientific Life)
MDs Urge Publisher to Sever Weapons Ties (AP)
Leading doctors criticize medical journal's link to arms industry (…
apalazzo | April 3, 2007Well I tried some weird experiments on my cells, injecting fluorescent DNA. The result is some psychedelic images. The cells clearly were not happy.
Here is some fluorescent DNA molecules that aggregated in the cell's cytoplasm. Cellular chickenpox?
Note that we are simply viewing the fluorescence - hence the black and white image.
Here is another injected cell with giant DNA aggregates:
For non-cell biologists I've outlined the cell nucleus and the cytoplasm. Note that these structures are not in the nucleus but rather are on top of the nucleus:
Here's a closeup of those weird DNA…
apalazzo | April 3, 2007It's nice to see scientific fighting discourse from the outside. I say this as a spectator wanting to see a fight, but as a scientist it makes me worried.
Yesterday I mentioned the John Hogan/George Johnson vlog about the Greene/Krauss debate on string theory on Bloggingheads.tv ... well there are quite a few commentaries about the whole recent episode.
Sean Carroll at Cosmic Variances is upset. I do agree with his view that public debate is good, but I have to say that he utters outrageous statements that as a scientist make me cringe.
I have a long-percolating post that I hope to finish…
apalazzo | April 2, 2007Finally. NPR has been providing almost all their content online for quite a while.
First you can watch Charlie Rose ... for free! (It use to cost 1$ a show, now you can watch the last week no charge.)
Now NOVA has some videos. Great!
Then if you want more see John Hogan (The End of Science) and science writer George Johnson talk about the Greene/Krauss debate on string theory they are on Bloggingheads.tv.
apalazzo | April 2, 2007I've been struggling with eIF4E. You see eIF4E is the major cytosolic cap binding complex. When mRNA is synthesized in the nucleus the cap is loaded with nuclear cap binding complex, CBP80/20. Then (the story goes) the mRNA is exported to the cytoplasm where the ribosome engages the transcript and thus the pioneer round of translation begins. If there are problems such as premature termination codons, the RNA is degraded by nonsense mediated mRNA decay (NMD). If all is well, CBP80/20 is exchanged for eIF4E and now full scale translational synthesis can begin.
How does eIF4E promote…
apalazzo | April 2, 2007In this month's edition of Mendel's Garden we present to you the latest from the home office in Brno: Mendel's Premium Fish Flakes.
Guaranteed to invigorate your favorite genetic model organism, these flakes will work wonders.
Here are some testimonials:
Coturnix is wowed about how his massive aquarium has benefited from Mendel's fish flakes. With the latest genomic sequencing techniques that are discussed in a recent issue of PLoS - Biology, he can now analyze the genetic diversity in every corner of his huge aquarium. Coturnix points out how different DNA sampling procedures could tell us…
apalazzo | April 1, 2007I have to admit this one is better than last week's post. Yo, TCA man, T-C-A.
[HT:Dario]
apalazzo | April 1, 2007A video of one of the most bizarre phenomena known to man. I believe that PZ Myers wrote his undergraduate thesis on this fascinating subject.
apalazzo | March 30, 2007There is a divide within the biological sciences, those that are concerned with proximal causes and those concerned with ultimate causes. For every question in biology there are two answers.
Ultimate causes have to do mostly with the "why?"s. Why was this structure selected for? But not always. What advantage did this gene give to the organism? Do synonymous mutations give a selection advantage?
Proximal causes have mostly "how" questions. How does this protein work? How does a cell cycle check point function? How does this synonymous mutation affect protein folding?
Another way of thinking…
apalazzo | March 29, 2007Tuesday and Wednesday Dr Neupert was here at the medical school. The topic of his two seminars was mitos.
It is amazing how many protein shuttling mechanisms there are in mitos. Mitos only make about a dozen proteins from their own DNA, the rest are synthesized from nuclear genes. These nuclear derived gene products have to be imported into the mitos and this is where all the protein transport comes in. There's the TIM and TOM complexes to shuttle proteins from the cytoplasm into the intermembrane space and matrix, the TOB complex the Oxa transport system, the stop transfer system all working…
apalazzo | March 25, 2007Quebec's provincial elections are being held tomorrow. I won't be voting in this one - my green card application is still under review, and I can't cross the border until all my paperwork is settled. Since the thee main parties are tied in the pre-election poles, it's likely that like the Quebec will have a minority Government, the first in over 100 years. As two of those parties are separatist parties, it's likely that poor Quebec will be dragged through another referendum within the next 5 years. That's the last thing that Quebec needs ...
Here's some info from the CBC.
Update:
G&M…
apalazzo | March 25, 2007No video, just 44min of audio on Popper, one of the great philosophers of Science. (No I don't stricktly hold his views, but his ideas are very insightful.)
It's interesting how Popper's ideas were shaped by the progression of physics from Newtonian physics to Einstein's relativity in contrast to the inflexible theories proposed by the Marxists and Psychoanalysts.
As for the second part, on Popper's Open Society, American conservatives should listen very carefully.
apalazzo | March 25, 2007Next week I'll be hosting the latest edition of Mendel's Garden, a blog carnival for genetics blogging. Despite the fact that I've been blogging for over two years and participating in many carnivals, this will be my first time as a host (not that your entries are parasites ...)
So send in your genetics related posts via email - I'll accept them until 11:59PM April 1st and the full carnival will appear here sometime April 2nd.
apalazzo | March 23, 2007from a stairway at Harvard Medical School.
Interesting tags ... just like street graffiti, scientific graffiti is probably meaningless to the untrained eye.
Here's a closeup:
Notice the greek slang (lambda for microlitres), the violent use of base to strip off antibodies, the reference to blood sacrifice (IVT), and the malefic use of calcium. I'm guessing that these were the work of a former Rapoport lab member.
apalazzo | March 21, 2007OK here's a refresher ...nuclear export of mRNA in yeast:
Nucleoplasm is on the bottom, cytoplasm on the top. The bilayered nuclear envelope is represented by the two black lines. The top line is the outer nuclear envelope the bottom line is the inner nuclear envelope. The big red/blue thing with the purple basket is the nuclear pore complex (NPC).
In green is the TREX mRNA nuclear export system (TREX = transcription, export). These proteins are loaded sequentially during transcription in yeast and during splicing in higher eukaryotes. In most cases the Tho complex, which is comprised of…
apalazzo | March 20, 2007Yesterday we had a look at the science funding sutation south of the border, today we look up north.
In their new budget, the Tories have allotted some extra cash for graduate-student scholarships and university research. The increase will amount to an additional 40% for postsecondary education which now stands at $3.2-billion per year. This includes 1,000 new scholarships for masters and PhD students. Remember, up north all the schools are public and so their budget is set in part by the federal and provincial governments. So in all it sounds good ... right? From the Globe and Mail:
The…
apalazzo | March 19, 2007Click here to watch now. It's over.
To read Elias Zerhouni's statement click here.
A pretty good presentation. Zerhouni was joined by some department heads (including our own, Joan Brugge).
Some highlights:
-The approval rate of first time RO1s by first time investigators is down from 15% in the mid 90s to 5%.
-Students are not entering science as they see a lack of opportunity.
-Investigators are spending more and more time writing grants and less time performing research and mentoring.
-High risk, high impact science is suffering the most. When budgets get tight, risky projects don't make…
apalazzo | March 19, 2007From the Metropolitan Diaries section of today's NYTimes:
I boarded the 57th Street crosstown bus at York Avenue and, as usual, inserted my senior citizen transit card incorrectly. The driver very kindly took it out of the fare box slot and reversed it before handing it back to me to reinsert. I sat down wondering why I could not master this simple procedure. True, I didn't use city buses regularly, but still ...
My seat overlooked the bus entrance, where I could observe boarders doing it right the first time without assistance. The large black bar went on the right, the cutoff corner on the…
apalazzo | March 17, 2007I adjusted my blog roll for the first time in ~6months, I'll do some more tomorrow. If you want me to list you, let me know. Also I added some new entries to the Taxonomy of Sciences. Two new outside entries + a bunch of genetics entries that I ripped off of evolgen.