More puffery about epigenetics, and my usual role as go-to curmudgeon
The word "epigenetics" once meant simply "development"—that is, the way the genome worked itself into an organism through the production and regulation of proteins and absorption of food and materials from the outside, and the turning of some genes on and others off in different tissues. Now, however, the term means roughly "forms of inheritance that rest on modification of the DNA sequence," and by "DNA sequence" I mean the sequence of four bases (A, G, C, and T) that constitutes the DNA code.
Open Acess books
As a software developer the most amazing thing are Open Source projects, they are just awesome, they are free and they work perfectly, projects like apache are just one of the great things about Open Source.
In academia/research there are also some “Open” stuff, we have Open Access. For example, I am in love with Plos one and InTech, Plos one is an Open Access peer review journal and InTech publish Open Access books.
Do you know of any other Open Access resources? I would love to check them out.
Finishing Linux installation
I was trying to install linux and it is done 
The guide proposed was a little outdated and not everything worked as smooth as possible but the information there was of big help. (Madman, thx again, great work)
To explain a little, the main problem was setting the NVidia video card in the Alienware M14X to, actually, work; after my first installation try the problem was I could not see anything because the NVidia card did not worked; to fix this the procedure I followed was:
- Install linux (ubuntu) with the power cord unpluged (so the NVidia card is not used)
- Update the ubuntu kernel
linux-headers*-all.deb linux-headers*generic*-<yourarchitecture>.deb linux-image*-<yourarchitecture>.deb
sudo dpkg -i <linux-headers all file> <linux-headers generic file> <linux-image file>
- Install Bumblebee
sudo apt-add-repository ppa:mj-casalogic/bumblebee sudo apt-get update sudo apt-get install bumblebee
Configuring bumblebee select “Mario Höllein” or “MadmanMT” profile configuration
- Configure the USB
ums-freecom.disabled
ums-sddr09.disabled
uas.disabled
ums-isd200.disabled
ums-sddr55.disabled
ums-alauda.disabled
ums-jumpshot.disabled
ums-usbat.disabled
ums-cypress.disabled
ums-karma.disabled
usb-storage.ko
ums-datafab.disabled
ums-onetouch.disabled
ums-eneub6250.disabled
ums-realtek.disabled
New Discovery channel series – Curiosity – great!
I just saw the first episode of Curiosity: Did God create the universe?, very nice episode. I love to see scientist saying things that are uncomfortable and outside of the box, people have relegated science to just explain things outside of religion, but this is a nice example how science can answer big questions and that we will have to adapt our beliefs with reality.
I recommend to watch it to everybody, its an amazing show
Part 1, part 2, part 3 and part 4
The episode does gives a simple answer to the question it ask, Did God create the universe? Well… simply, No.
(I also recommend watch the discussion after the show, scientists and scholars giving opinions about that answer: Panel part 1, part 2)
Installing Linux
Update: This post was for Ubuntu 11.04, I updated my system to 12.04 and it is still working perfectly.
_______________________
Well, I just changed my computer. My old MacBook pro got its logic board burned (damn macs!)
Searching for a new laptop I decided I wanted to buy a MacBook pro of 13″ or a new m14x Alienware. Well, my decision was easy, apple, for some reason, sells computers in Europe at the same price than the US but in Euros, that means: a US $1200 computer becomes a EUR$ 1200 computer = US $1700 … kind of expensive for what you are buying. Does anybody knows why? Is just for making more money? Is because of the taxes? Is because apple is now an evil corporation? I would appreciate if anybody knows…
Well, then, I needed to install Linux. I didn’t check anything before hand because I thought: ”Who in this world would make a computer incapable of running Linux?”… well… what a surprise! As a matter of fact, the Alienware laptops have a HUGE problem when you are installing Linux, I tried installing Ubuntu 11.4 as any normal person would, but then, after restarting something strange happened to my monitor: half of the monitor was black, the other half was white with small black stripes. The reason? You don’t want to know… nvidia optimus does not work for linux and Alienware bios do not allow to disable optimus (thanks alienware and nvidia, you fucking rock! )
But everything is not bad, thanks the FSM for internet. I was not the first person having this problem (obviously) and there was a “madman” who was capable of installing linux in his m14x, I will be following his guide and will write about how everything goes.
The guide: Linux installation thread
here’s how i did it.
Install ubuntu x64 11.04 with the power adapter unplugged.
when you will have to reboot, if you are lucky you will see the interface, when i got the screen display issue i had, i had to shut down completely and wait then open a terminal and do the following.
How To Update Ubuntu 11.04 Kernel To 2.6.39-0
This will install the 2.6.39-0 kernel. You will reboot, then get the bumblebee project.
you will do sudo apt-get install git
then do the following
git clone https://github.com/MrMEEE/bumblebee.git
then go inside the bumblebee directory and do
sudo ./install.sh and follow the instructions
when you get promped for which laptop to use, choose 1 which should be the L502X.
then, to use your applications with the nvidia card, run optirun32 or optirun64 application name
If you are going to do it, read the whole thread, it is not long and in it they also talk how to fix the USB3 and other stuff
Well… just to end, to madmantm: tank you! to Dell (Alienware) and Nvidia: grow up! Some people need linux… ok?
eQTL for Dummies – Usefulness
Now that we know what an eQTL (expression Quantitative Trait Loci) is in broad terms, we can discuss “why” we would like to make an eQTL analysis.
We all know about the existence of genetic diseases, also we know that those diseases are produced by some differences on the DNA (thats why they are called ‘genetic’). It’s not difficult to imagine that if we need some protein complex to do a specific job but some of the genes (the DNA sequence) that produce some of those proteins have changed, then the whole complex could cease to work or at least work differently. This is what happens in cancer cells, in some types of cancers, for example, the genes that control the process of apoptosis (cell death) get screwed and those cell just don’t ‘hear’ the body orders for them to die, and there you go… cancer!
So, what do we have? First, a complex disease that we don’t fully understand which have so many variables we don’t know where to start looking, and second, the possibility that those variables are not all related to just changes in the coding sequences of the DNA. In that second possibility is that eQTL analysis comes into play, what we are going to look for is that maybe the protein complex is not working as it is suppose to work not because there is something wrong with the parts, but because there is something wrong with the number of parts.
Let’s make an example, imagine a car, if the car stop working it can be for many different kinds of reasons, like a bad engine, no gas or it is stuck on the sand, who knows, so many possibilities! So, imagine a common problematic part of the car, the tires; what is your first guess? flat tires!? Maybe, we can presume that the tires are flat and we just need air to inflate them again, you may see this as our first approach, one of the necessary parts of the car is broken (similar to “there maybe some non-functional protein, lets search for the change in the DNA”) but, could it be that the problem is that there are only 3 tires? That’s an expression problem, the problem is not that the tires are flat, there are 3 beautiful, inflated and perfectly working tires, the problem is that we need four!
Going back to diseases, there are genetic diseases in which the problem is a difference on the amount of proteins working for a process, an those problems are not related to difference in the coding region of any protein but in genetics factors related to gene expression.
Ok, very altruistic, right? we want to help to find a fix to every genetic disease, but, actually, we also want to understand the relation between genes, just for the hell out of it (not really); we want to know how the expression or regulation of some genes make other genes to be expressed or regulated, eQTL analysis also helps us with this. After looking the behavior of gene expression in some diseases we have more information about what genetics factors are associated with what genes, we call that information “markers” and for markers produced by eQTL we call them eSNP, and with this markers and other markers giving information to GWA (Genome Wide Association) studies we can better predict the risk for diseases and better understand how those diseases will try to kill us.
eQTL for Dummies – Intro
What the hell are eQTL (expression Quantitative Trait Loci)?
Let’s start by the beginning, What is a “quantitative trait”? It’s any phenotype that can be quantified, in other words, anything we can measure about the phenotype of a given organism, e.g. we can measure height, fat, skin color, etc, etc. any of those can be a quantitative trait.
Ok, easy enough, but what is a “quantitative trait loci” (QTL)? It’s a quantitative trait -a measure of the phenotype- that is associated with a particular loci, in normal human language: QTL are phenotypes associated with a sequence in the DNA. That DNA sequence have a direct effect on the measure of phenotype, taking the ‘fat’ example, suppose that if you have a determined sequence in your DNA sequence, you will have more or less fat that if you don’t have that sequence.
What about the expression? We are talking about the expression of genes, how much of each gene is being produced by the target cells. So, a quantitative trait is anything we can measure, can we measure gene expression? Off course we can! That’s what microarrays are made for, that is their whole reason of existence.
To conclude, we are measuring the quantity of genes produced by each cell and looking if those changes in expression of the genes can be because of a given DNA sequence.
What are eQTL useful for?
