bsod’s braindumps

Moleculair Biology

Core of Molecular Biology

All living species are made out of one or multiple [cells]. In all species, the genome is passed to the next generation through DNA, hence the importance of DNA. DNA is [transcribed] into RNA, which in turn is [translated] into protein. The function of proteins is the core of biochemistry. The function of genes is the core of genetics.

Central dogma of molecular biology - The standard information flow pathway can be summarized in a very short and oversimplified manner as “DNA makes RNA makes proteins, which in turn facilitate the previous two steps as well as the replication of DNA”, or simply “DNA → RNA → protein”. This process is therefore broken down into three steps: [transcription], [translation], and [replication]. By new knowledge of the RNA processing, a fourth step must be included: [splicing].

The Last Universal Ancestor is the hypothetical common ancestor to all living cells, and would be the earliest cell conforming to the Central Dogma. It is hypothesized that the last universal ancestor already had all of the properties that are shared by all currently living organisms, such as a prokaryotic cell structure, DNA, the modern genetic code and mRNA, tRNA and ribosome mediated transcription.

Exceptions to the Central dogma - The biggest revolution in the central dogma was the discovery of retroviruses, which transcribe RNA into DNA through the use of a special enzyme called reverse transcriptase has resulted in an exception to the central dogma; RNA → DNA → RNA → protein. Also, some virus species are so primitive that they use only RNA → proteins, having not developed DNA. With the discovery of prions, a new exception to the central dogma has been discovered, Protein → Protein. That is, proteins directly replicating themselves by making conformational changes in other proteins. Although retroviruses, certain primitive viruses, and prions may violate the central dogma, they are technically not considered “alive”, and thus the rule that “all cellular life follows the central dogma” still holds true.

Prokaryote and Eukaryote cells

The difference between the structure of prokaryotes and eukaryotes is so great that it is considered to be the most important distinction among groups of organisms. However, The three-domain system is a biological classification introduced by Carl Woese in 1990 that emphasizes his separation of prokaryotes into two groups. Woese has proposed dividing prokaryotes into the Bacteria and Archaea (originally Eubacteria and Archaebacteria) because of the significant genetic differences between the two. This arrangement of Eukaryote, Bacteria, and Archaea is called the three-domain system. The three-domain system was quickly adopted by most molecular systematist.

Prokaryotes are organisms without a cell nucleus (= karyon), or indeed any other membrane-bound organelles, in most cases unicellular (in rare cases, multicellular). This is in contrast to eukaryotes, organisms that have cell nuclei and may be variously unicellular or multicellular. Most prokaryotes are bacteria, and the two terms where often treated as synonyms (before the arrival of the three-domain system).

Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound a cell nucleus. They include the animals, plants, and fungi, which are mostly multicellular, as well as various other groups collectively referred to as protists, many of which are unicellular. In contrast, other organisms such as bacteria lack nuclei and other complex cell structures, and are called prokaryotes. The eukaryotes share a common origin, and are often treated formally as a superkingdom, empire, or domain.

In humans, around 97% of the DNA is regarded junk DNA, which are introns in genes. introns also play a part in the transcription from DNA to RNA. A promoter is a DNA sequence that starts the DNA->RNA transcription. 45% of th human DNA is supposed to exist of Selfish DNA.

The entire DNA->RNA->protein process, tho common in all life, is very different between eukaryotes and prokaryotes, where the genetic code between the two differs, sometimes DNA is completely absent from certain prokaryotes and virusses.

Moving from 32 to 64 bits

Windows Vista will mean several things: DRM, 64-bit multicore processors, more than 4GB memory (true 64-bits, ddr3), and DirectX 10.

C/C++ compilers generate great assembly code, but sometimes you want to get down to the metal and do every instruction yourself. Under the x86 architecture, this usually means you want to do specific MMX/SSE stuff in your application.

compiler code generation

To support modern architectures, you basically need to recompile. x86-64 issues are handled by recompile for that architecture, sse2 stuff requires your compiler to be very good at vectorizing code, and multi-core is handled by using multithreaded coding (Boost.Threads, for example).

x86-64

Most issues are straightforward, but there are a few big differences. First of all, the x87 floating point is not supported under amd64. You must use sse2. Secondly, the 64bit version of MSDEV does not support inline asm anymore. gcc however obviously supports inline asm. In either case, you can use fasm for 64-bit asm modules.

Clijsters rules the planet

I never dreamed of this, but Kim made #1… She is now officially the best female tennis player in the world!!! Davenport lost against Justine *hugs Justine* and Kim won against Martina Hingis. So. Let’s hope she wins Melbourne, but frankly, she doesn’t really have to, IMHO. Just take care of that back injury and have a good time in general.

Great joke about Blondes

I hate blonde jokes normally but this one is really good

Crashed

Arghh nooo… I wanted to create some diskspace for Qemu disk images by deleting my Ubuntu partition when right after pressing the ‘delete’ button I realised that grub was on this linux partition. Uh-oh.

NTLDR not found.

Okay. This sucks. Windows Recovery Console and type ‘fixboot’ and fixmbr’… no luck. Reinstall Linux on the partition and reinstall grub… no luck. Install the Freebsd bootloader…. no luck.

I’m using Ubuntu right now to type this, and am busy copying away the various backup files of the dead system.

Qemu for Windows

I’ve installed qemu 0.8.0 for windows yesterday, and installed windows XP on it. It works like a charm, but I’m still working out the details on the network device.

Iran

Why is Iran persuing nucleair weapons while the entire world doesn’t want them to?

First of all, Iran wants to walk the path of international negotiations, but to take a hardline stance at the same time. The U.S. is strong, but not as strong as it appears. Wars cost money, and Iraq is proven to be a very costly war. America’s foreign debt currently standing at $8,184 trillion will hit the debt ceiling as early as February-March 2006, according to the pravda. I don’t see any other country taking action against Iran, except maybe Israel, who could just bomb the nucleair facilities of Iran and get it over with. They are already at war with the rest of the Middle East, so who cares. It’s not a fun thing to do however, and I’m sure a lot of Israeli won’t like this deed of agression. However we all know where Iran’s bomb is going to fall when they make one, so… how much choice do they got, really?

The problem is that Iran will probably declare war on Israel, and that’s no fun. Iran is a mountainous country, and probably impossible to conquer, unlike Iraq. And Israel doesn’t want war, it wants peace. *sigh* Let’s hope it all settles down, somehow. I don’t see how, however, but that’s just me.

Withdrawal from Iraq

I’ve been reading an article on aljazeera, which tells a few interesting things: firstly, that there are now *less* iraqi forces battle-ready than there where a few months ago, and that it will take several years to give these men the battle experience they need to actually win some kind of conflict. In short: the Iraqi suck as warriors, much like the Dutch do. Another interesting point in the article: ‘It is understood that the majority of Iraqis want the Americans to leave. That wish is shared by the majority of Americans.’

When you think about a little while, you’ll realize, like me: This is another example of “It makes no sense anymore to wage war against eachother, it only makes loosers out of everbody involved in the conflict.”

I don’t think that increasing the amount of U.S. troops in Iraq will be the best solution however, as this article states. The problem in Iraq is the total absense of security in the country, and I really, really doubt that increasing the amount of soldiers running around in the streets is going to do anything about it.

What is needed is more ‘Smart Soldiers’. When your enemy is hiding, small in numbers, well funded, and willing to commit suicide for tactical reasons, you’re in a different kind of warfare. So you need more Special Forces, more intelligence. It’s not the first time this kind of war exists. Stalin supressed insurgencies, the germans in WO-II did it. Attila the Hun could do it. It’s no rocket science to suppress the people. The art is to give the people a sense of freedom, food, wealth and democracy while staying in firm control of the power. Good luck GWB. We all know you can do it.

DVD ripping under Windows

To rip dvd’s I’m currently using DVD Decrypter to rip and descramble the movie to .VOB files on the harddisk, MPEG Mediator to make one mpeg out of all these .VOB files, VirtualDub to resize and manipulate this mpeg file, and Flask MPEG to render it into a divx/xvid .avi file.

I’m not really happy with all this complexity, but there is a lot of flexibility using this pipeline approach. All these programs have their downsides, and for all of these there are alternatives. For example, you could use AnyDVD instead of DVD Decrypter. Things like Alcohol 120% and Nero Burning ROM are also essential, and Adobe Premiere Pro is also nice to have.

Bad ideas

On edge.org, there is an interesting link to an article where prominent people tell their most dangerous ideas. In 2005, they where questioned about What do you believe is true, tho you cannot prove it?… also an interesting read.