Appreciating Randomness...E.coli Interupted

[mycrap]
Presenting a classic problem in genetics...a great way to introduce oneself to Mr. Poisson (of the distribution fame)...the joy of modelling...
[/mycrap]

Problem: The transfer of DNA from Hfr begins at oriT. The gene closest to oriT on the donor chromosome enters the recepient cell, followed by successive genes on the donor chromosome. The frequency of a particular gene entering the recepient is a function of its distance from oriT. Moreover, this frequency is found to decrease "exponentially" with a gene's distance from oriT. Why is this decrease exponential (and not linear, say)?

The Solution:
Poisson says

"Let m = the mean number of successful events. The probability of k successful events is given by the formula -
P(k) = (e^-m * m^k) / k!"

The key to solving the given problem is to define the 'm' value. Let us define the m value as the 'number of breaks per unit length of the chromosome'. So if 'x' is the length of a given chromosome segment the number of breaks in x will equal 'mx'. Remember that mx is the average number of breaks in a population of chromosome segments of length x. That is some x-lengthers will have more that mx breaks and some less than mx and some may even have zero breaks.

Even a single break in a length x is sufficient to ensure that a marker at distance x from oriT is not transferred. In other words any non-zero number of breaks in x will prevent marker at x from being transferred.

Now consider a circular ds DNA E.coli chromosome. Consider markers located at distances x1, x2 and x3 respectively from oriT.



What are we distributing? Good question. We are distributing 'breaks' to x-length chromosome segment populations.






In case of x1-lengthers,
P(0) = Probability of having 0-break x1-lengthers = e^-mx1
P(1) = Probability of having 1-break x1-lengthers = mx1 * e^-mx1
P(2) = Probability of having 2-break x1-lengthers = (mx1^2 * e^-mx1) / 2
P(3) = Probability of having 3-break x1-lengthers = (mx1^3 * e^-mx1) / 6
.
.
.

Now comes the good part..

We are interested in whether a marker within distance x is transferred. It will be transferred if there are zero breaks in the length x. Hence we are interested in the fraction of those x-lengthers which have zero breaks. We are interested in the zero term P(0).
P(0) = e^-mx1

Similarly, fraction of markers at x2 transferred to the recepient,
P(0) = e^-mx2 and
fraction of markers at x3 transferred to the recepient,
P(0) = e^-mx3.

If we plot the values of P(0) for x1-lengthers, x2-lengthers and x3-lengthers versus the distance x1, x2, x3 then obvioulsy an exponentially decaying curve would be obtained. Multiplying the P(0) values of each by the total colonies scored will give the expected number of colonies recombinant for these markers, decaying exponentially with each's distance from oriT.

Now Playing in Kopete...

Hi,
Follow these simple steps to display the song currently playing in XMMS as your status in Kopete.

1. Create the following script - kopete-status.sh

#!/bin/sh
STATUS=" `current |awk '{ print substr($0,index($0,":")+2, index($0,"(")) }'` "
dcop kopete default setAway "$STATUS"
echo "Kopete Status: $STATUS"

2. Issue chmod u+x kopete-status.sh to make the script executable and then finally issue
watch -n 5 ./kopete-status.sh.

We r done. Watch your Kopete status being updated every 5 secs to the song being played in XMMS.

Note: U must have this package also: http://www.xmms.org/files/plugins/xmms-extra/xmms-extra-0.1.tar.gz

The Devil

I once heard someone important say "In biology, the devil lies in the detail".
Biology has since long become inter-disciplinary and is becoming even more so. Clearly, assuming that one has the analytical skills, more the number of facts one knows the better off he would be in biology.

It seems like until now I gave the devil a lot of free play.


Time to kill the devil...

Bottom Up

He who would study organic existence,
First drives out the soul with rigid persistence,
Then the parts in his hands he may hold and class
But the spiritual link is lost, alas!

--Goethe (Faust)




P.S. Those four lines . . . Well. Goethe says it all.
Nothing less. Nothing more.

Vacation at Binsar

7 days of fresh air
7 days of royal cuisine
7 days of long winding drives
7 days in the wilderness
7 days in the valley
7 days amongst the rivers
7 days of exotic countryside
. . .

Ok. Thats it. Back to Mumbai.

9:29 Churchgate slow . . .

Applause

I had blast!
Finally delivered the seminar today. Things went pretty smoothly.
I used the LCD projector for the first time. I loved every aspect of it. I did all the connections, wiring, setup...typical geekstuff.
There was no technical snag. But my own laser-pointer defied me :(
The words flowed out magically. I managed to convey atleast 50% of what I was saying. Partly becuse the 2nd half was kinda drab...perhaps too geeky for the un-enchanted-by-how-things-work.

I particularly liked my end-note:
"Our civilization has always been struggling to build tools which help us to measure time. First came the sand-clock, then the pendulum based ones and recently we have these hi-tech atomic clocks. But, ironically we all - the biologicals have had, right from the beginning an internal biological clock which keeps time faithfully. And now this clock [pause] this process has become aware of itself !"

A Simple Java Code

Code

import java.util.Vector;

public class MyCodons{

//globals
Vector codons = new Vector();
String[] bases = {"a","g","c","t"};

//fill the 'codons' vector with values
public MyCodons(){
for(int x=0; x<bases.length; x++){
for(int y=0; y<bases.length; y++){
for(int z=0; z<bases.length; z++){
codons.add(bases[x]+bases[y]+bases[z]);
}
}
}
}

//display the 64 codons
public void printCodons(){
System.out.println(codons.size()+" possible codons\n"+ codons);
}

//main method
public static void main(String[] args){
System.out.println("Generating codons...\n");
MyCodons obj = new MyCodons();
obj.printCodons();
}
}

Molecular Logic: Biological Time Keeping

Going to give a seminar in the coming fortnight. We were given the freedom of choosing our topic. This topic hunt was something that I enjoyed.

I was reading a book 'Fly' - in which drosophila has been glorified as 'the' tool of molecular biology research. I stumbled upon a chapter on circadian clocks and got hooked. Drosophila apparently is the ideal model to study molecuar logic of circadian clocks.

The clock basically consists of three modules - the light input component, the oscillator and the output component. I am especially fascinated by biological light sensors, the first component. The idea that a clock can be implemented using transcriptional feed-back loops is really interesting, the second component. The role of the clock in organismal behaviour, the third component, immediately implies that this clock is not just another clock but an important control in organismal behaviour.

It seems that even a single aspect of this little insect, its clock, has a lot to offer. I should'nt have any problem gathering material for my upcoming 1 hr. speech.

Following is one of the interesting links I found on the web:
http://www.scienceden.com/mbiology/research/circadian

P.S.: The flash on this site is very helpful. As someone important has said "If a picture is worth a 1000 words what do you say about a moving picture !"

H'ppy B'day 2 Me

I feel good tarara ra ra ra...

Went to the Institute. Had no lectures today. Just had a stupid practical - Biuret Qualitative Analysis. Distributed Perk XL to buddies.
Came home. Mom had made mango and strawberry ice-cream. Enjoyed four scoops.
I really feel special.

Its good to be me.

Tom's Favorite Quotes and Mine Too

I was on a Google spree. Stumbled upon his really awesome collection of quotes.
Its a must read.
Tom's Favorite Quotes

P.S. Dont forget to listen to:

• fennyman's voice
• "Back off man, I am a scientist" - Ghostbusters. [ lmao ]

'Sound' Synthesis

I was thinking of an approach to do synthesis of sound - 'synthesis of voice' to be precise.

I have made few basic assumptions upon which the sound synthesis approach will be based. They are -

• speech is not continuous but it is made up of discreet elements.
• each individual has his own 'library of sound elements' from which s/he assembles speech.
• a library has one atrribute - number of elements (size).
• each element also has one attribute - the sound (note) which we hear.
• the libraries of any two individuals are of same size and contain the same types of notes.
• two analogous notes from any two different libraries differ only slightly so as to accomodate the fact that no two voices are same.
  

More to come ...

Such Extravagance! I know

*
Shopping Spree ... Went shopping for a Nokia 6600 for Rajas.

* Courtesy Rajas's 6600. Of course, Rajas is behind the lens.

My First Post

Greetings people !!! :) Signed up for a Blogger account. I think the 'polka' theme really suits me. That is ME.