Archive for November, 2007

comparative genomics

Wednesday, November 28th, 2007

There is a good paper on comparative genomics and structural biology by Aravind et. al..

Comparative genomics and structural biology of the molecular innovations of eukaryotes
Current Opinion in Structural Biology Volume 16, Issue 3, June 2006, Pages 409-419

Extreme accumulation of nucleotides in simulated hydrothermal pore systems
Philipp Baaske, Franz M. Weinert, Stefan Duhr, Kono H. Lemke, Michael J. Russell, and Dieter Braun
PNAS | May 29, 2007 | vol. 104 | no. 22 | 9346-9351

To be continued

Finally, I’m on Fedora 8

Friday, November 16th, 2007

I thought that very new release of Fedora should be much better than previous one. Well, I should have said that it is just a dream. Since FC5, I’ve always had problems with wireless on my Dell B130. I never figured out it at all. That was why I’m always eager to upgrade. It turned out just broken hearts.

This time, Fedora 8, it is even worse. I couldn’t install it at all! It just stalled at very beginning with

running install …
running /sbin/loader

After struggled for two days, I just learned another tip of Linux. Hit “Tab” before select the “install”, and then add “nohz=off nolapic” to the boot command. Problem solved.

There are many things in Linux that I need to learn, even very true for a “senior” Linuxer. Another challenge is how to fix my bcm43xx wireless. It is a headache now.

[Continued] My wireless was fixed by Krishna, I know very few of what he did. all I know is that he used “b43” and a firmware cutter to get the driver. Now my wireless works like a charm.

An interesting talk on stress signalling

Thursday, November 8th, 2007

There was an interesting talk by Tsonwin Hai at the Beadle Center. The take-home message is that stress signals in different contexts trigger a variety of initial genome response. The ways of response from cell differ in the cellular context. The final consequence of the stress and response is maladaptation state or disease. Her figure in the text form is here:

stress signal [stress context]
->
initial genome response
(diversity) [cellular context]

-> -> ->
maladaptation [disease]

Why do we compete and what for?

Thursday, November 1st, 2007

We heard a lot, and actually have vividly evidenced many that being competitive is good. The reason is exclusively simple, we all want to have joy. People argue the definition of joy much more than, if at all, the reason itself. Let’s leave the task of defining joy to humans, what is the nature of competition for other lives, such as, bacteria, plants, spiders, …? Why do they compete and what are they competing for? It has been argued a lot by those formidable philosophers that every object (almost) ought to be studied from both inner and inter parts of the object. Pretty scary. :-(

I’ve read an essay by Steven Frank and he presented the competition of life in a very elegant way. I can’t help quoting what he wrote in his essay published on Current Biology.

Sociality means living in groups. Group living intensifies two opposing forces. On one side, proximity exacerbates conflict for local resources. On the other side, cooperation with neighbors may enhance group efficiency and aid in competition against other groups.

Down to the bottom, in terms of social life conflict and cooperation are the basic requirements of life. Multicellular systems are not exceptional. What can we learn from this sociality perspective so that we could have better understanding of molecular development? As Steven pointed out. Slime mold could be a good model to answer this question. Slime molds live as single cells in most of their lives. Although it is rare, some cells do aggregate to a degree that two tissues are developed. One is spore, which is the result of the growth of reproductive cells and the other is stalk, which is the result of the somatic cells. We then have an potential killer example of observing conflict and cooperation which can be examined in lab. This article is surely worth recommendation!

Are we human the consequence of the competition both mentally and physically? Or we are in the precess of something else? scary, enh? :-(