The celebration of a mother’s mercy

So it has been 32 years since God brought me into this world through my beautiful mother. I only remember bits and pieces of what happened before today, but among the strongest memories that stay with me is the mercy and love of my parents.

I don’t really know when people started celebrating their birthdays, but as with every event that God gives to us, it’s a good time to reflect and be grateful. Obviously, I have been blessed with so many things. And if I try to enumerate them, no doubt I will not be able to do so. Yet O so often have I forgotten about them and set my focus only on things that I don’t have instead. Shame on me!

But anyway, as with any birthday, the credit and congratulation should go to the one who deserves it the most, which in this case is the mother.

In labor, every mother risks her life to deliver a human being into this world. It started with 9 months of difficulties and exhaustion, which in many cases deter many parts of her body. After birth, the baby will need to be nurtured and taken care of until he/she reaches independence, which takes many years and immense effort. But the mother (and father) will never yield, and will continue to support the person who was once her little baby, even though she doesn't get the gratitude that she deserves.

The Prophet (peace and blessings be upon him) said that after God and His messenger, the mother is whom we must respect the most. She has done so much for us, that nothing we do will ever repay her mercy. Even the best deed that we do for her will not even recompense the pain of giving labor.

So I take this opportunity to express gratitude for one of the most immense blessings that He has given me.

Thank you mama and papa, for showering your mercy upon me. I most definitely did many bad things. Yet you continued to support and care for me. May God also shower mercy upon you as you showered mercy upon me when I was feeble and weak. 

Installing DOCK 6.1 on mint linux

For people who are new to the UNIX system, installing programs manually can be a daunting task. This was indeed the case for me anyway. I needed to install some molecular modeling softwares such as GROMACS and DOCK from UCSF, and I had a hard time doing so.

For GROMACS, it was a straight forward task, as it was available in the mint linux repository, and other important components for the installation was automatically added. It wasn't so for DOCK 6.1, because I needed to install it manually and prepare the prerequisites as well, and I had to go through many trial and errors.

After googling and looking into several forums, I finally got DOCK 6.1 to work on my virtual mint linux (installed in windows 7). The summary of the procedures that I did, from unpacking to installing DOCK is as follows:


     tar -zxvf dock.6.1_source.tar.gz
     cd dock6
     cd install
     su
     --> input root password

In order to install the required compilers and other prerequisites, I needed to run apt-get. Unfortunately, because I am behind a campus proxy, I wasn't able to do it normally, so I had to find a way around it.

     -->(in su mode)
     export http_proxy=http://proxy.campus.net:8080
     apt-get install build-essential flex bison gfortran

     --> change g77 to gfortran
     --> go to the /usr/bin/ directory
     cd /usr/bin/
     ln -s gfortran g77

     --> go to the dock6/install/ directory
     ./configure gnu
     make all

--> in case of any "error: 'strlen' was not declared in this scope" errors, insert following lines in the mentioned .cpp files using a text editor:
     #include "cstdlib"
     #include "string.h"

--> Finish the DOCK installation

This did the trick for me, and thank God, I am now able to run docking simulations using DOCK with no hassle.

Adding PATH of directory in mint linux

I spent several hours trying to figure this out. There are so many resources in the internet that it is often difficult to get what we really need. I am writing it down here in case I forget again one day (or if anybody is experiencing the same problem).

Some suggested modifying the .bashrc files, some suggested to modify the etc/profile file, but what worked for me was by modifying the "environment" file. I just searched for the environment file using the search facility of mint linux's finder, then modify it by adding my directory path. 

From PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" 

to 

PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/fendrri/modeling/dock6/bin"

 Logged out, logged back in, and I was able to execute all the files within my target directory. Nothing fancy, but it worked out for me.

Insulting other people’s deities / gods

As human beings, we will always differ amongst ourselves, from small things to the big, likewise. This is true, including when it comes to what we believe in. All of us have a degree of certainty in what we believe in, based on what we know and understand, despite it having the possibility of being right or wrong.

At times, our differences can cause friction and tension between us. It’s natural, as long we don't go overboard with it. But unfortunately, we often do (go overboard with it). In the name of freedom of speech, we often disrespect and insult the party that we differ with. So much so we curse that what is most sacred to our opposition.

We see this all the time. As a Muslim, I often feel angry, sad and depressed when people mock at what I believe in. This feeling is perhaps mutual amongst Muslims everywhere. And unfortunately, instead of giving a noble response (to explain clearly why we are offended and try to build bridges to eradicate the misunderstanding), we often get trapped into becoming as bad as the people who insulted us, i.e. we also insult what is sacred to them.

It is a common sight where burning or abusing the national flag becomes a form of retaliation towards insults by a person of a certain nationality. I remember a couple of years ago when the infamous comics from Denmark came out. Muslims were understandably angry and hurt by the incident. But it still doesn't justify acts of flag burnings and the sorts.

We are strictly ordered to not insult or mock what other people deem as sacred, and the national flag is one example. Many people still deem the national flag as a kind of deity that they worship (consciously or not). The Olympics that is taking place is a testimony of this.

What is most important is to try and build bridges and introduce Islam to people who are misinformed. But this is an impossible task to accomplish if we ourselves are ignorant of what we say is our way of life.

The blessed at our doorsteps (song)

I have posted this as a poem in a previous post, but this time I have made it into a short song. I hope it can be enjoyed.

The blessed at our doorsteps

You have come you have come, o honorable guest

To wash our sins away

You have come you have come, as a blessing and a test

To reach for His love we may

You prevent us from our evil, and shine bright the good that we have

Locked away are all that’s deceitful, so everything is up for grabs

You have come you have come, o blessed nights

Filled with remembrance

You will come you will come, o night of might

May we not let you pass us away

Therein we received our guidance, the Book which in it there’s doubt

The emergence of a nation, the nation of he who we love

Will you stay will you stay, o blessed days?

In our hearts forever

Will we meet you again in another time and place

Our beautiful Ramadhan

The three types of people seeking sacred knowledge

Sacred knowledge of the religion is no doubt the most important knowledge that any human being could gain. All the physical sciences that one learns, without being coupled by sacred knowledge of the religion, cannot make someone closer to God. And in truth, to get close to, serve and please God is the only reason we exist.

Seeking sacred knowledge is an extremely praised act. However, this act can in fact destroy the person seeking it IF he does it for the wrong reasons. I am paraphrasing from a lecture I heard given by Ustadh Yahya Rhodus (may God preserve him) of Zaytuna, on the categorization of seekers of knowledge according to Imam Al Ghazali (may God have mercy on his soul) in one of his books.

The first type is the one that will be destroyed by his knowledge. These are the types of people who seek for sacred knowledge for purposes of this worldly life. They seek for knowledge for their career, to look good in front of other people, to debate other people with the knowledge that they have, and other worldly gains. These people will not get closeness to God through their knowledge.

The second type is the one that seeks knowledge to get close to God, but sometimes has the tendency or is tempted to use sacred knowledge for worldly matters. This is a dangerous position, because there is a possibility that he will get sucked into becoming the first category.

The third type is the best type, which is the one who seeks knowledge only for the sole purpose of bettering himself and getting closer to God.

Of course we should all aspire to be among the third type. But sometimes we are unsure about what group are we in. One way to check one’s self is through other people’s praises. If we feel good when other people praise us for what we know, then we are most likely in the first or second group, and need to get our acts straight.

May we all be true seekers of sacred knowledge, and have a noble rank with God.

A beautiful palindrome

Playing with palindromes is a fun thing to do. In case you’re not familiar with what a palindrome is; they are words or phrases that read the same in both directions. There are even some instances when the DNA sequences in organisms are palindromic. Several simple words that are palindromes are POP, MOM, EYE, RACECAR, and many others.

As you can see, even if we read the words backwards, they stay the same. However, when it comes to creating a phrase or a sentence, making palindromes can be a bit difficult. Some examples can be found in this website. 

Talking about palindromes, we can also find some in the Quran. Among them is in Surah (chapter) Al Mudathir (the cloaked one). The phrase is translated as “magnify the greatness of your Lord!” In Arabic, it is:

The letter in the beginning of the sentence means “and”, and is similar to a capital letter in our sentences. So broken down, the phrase becomes:

ر ب ب ك ف ك ب ب ر

which is also a palindrome, and an amazing one indeed, as it goes along with the context of what is being emphasized = to magnify the greatness of your Lord.

When constructing a palindrome, one must at least know the letters he/she is using and form them into a sentence. You can even try making one and find out that it’s not as easy as it seems. However, the palindrome in the Quran that was just mentioned was recited by a man who didn’t even know how to write or read.

Whenever the Prophet received revelation, he would recite it to his companions and it would spread as it is, without any auditing whatsoever. Furthermore, bear in mind that the Quran was orally transferred, not in writing. The palindromes and linguistic marvels in the Quran were not even recognized until linguistic scholars began to delve into it. 

So we can try to make palindromes with the language that we are best at. But no matter how hard we try, or how good we are with the language, we probably would never be able to create a palindrome as beautiful as the one in the Quran that was just mentioned.