Friday, December 28, 2012

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. 

Thursday, November 08, 2012

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
     --> 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=
     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.

Monday, November 05, 2012

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" 



 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.

Friday, August 03, 2012

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.

Monday, July 30, 2012

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

Friday, July 27, 2012

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.

Wednesday, July 25, 2012

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.

Monday, July 23, 2012

And they called him (peace and blessings be upon him) crazy

Preaching something new (or forgotten) can be an overwhelming task. This is especially true for the Prophets and Messengers (peace be upon them all). After all, what they preached was something that would radically change the fabrics of the society. It was so simple yet so fundamental that people would understand it, but refuse to accept it because of its consequences. It changes the way people would view the world. That God is one and worship Him, obey Him.

Thus, the Prophets and Messengers (peace be upon them all) had oppositions. Usually the rich and the powerful would oppose. Sometimes the whole nation would oppose, leave a few who accept the message. Those who oppose would use character assassination to distract people from the message itself. These opponents would call the Prophets and Messengers as magicians, poets, and even worse, they would call them crazy. While in truth, these Prophets and Messengers are from their own people. And the people always knew they were upright, truthful and just. Having better character than everyone else in the society.

This was also the case for the Prophet Muhammad (peace and blessings be upon him). He was given the name Al Amin, the truthful, and everyone knew about his noble character. But when he started spreading God’s word, his opposition called him crazy. But, God gave the Prophet consolation. Reassuring him that he is not. In fact, God revealed that for the Prophet, there is endless praise. It may not have made sense for the opposition at the time, but it sure makes sense now.

After more than one and a half millennia, the Prophet (pbuh) is indeed praised without end. There is no human being on earth that is praised more than him (pbuh). Now there are 2.1 billion Muslims all around the world. And all of them (well most of them) when being recited the name of the Prophet will say “Shallallahu ‘alaihi wa salam”, may God honor him and grant him peace. Muslims praise him in their daily prayers, and because of the time difference between different regions, it is most likely that there is always a Muslim praying somewhere, praising him while doing so. And Muslims all around the world, not even ever meeting him, would burst to tears when remembering him, and long to meet him.

What God has promised is the truth. And no, he (peace and blessings be upon him) is not what they said he was (crazy).

Sunday, July 22, 2012

Gathering with our loved ones… forever

Of all the blessings that God has blessed us, many would say that the blessing of family is one of the greatest. God has put in our hearts immense love for our family, especially our children. The story of Jacob and Joseph (peace be upon them) is one example of such love, where Jacob lost his sight due to extreme sadness of losing Joseph. This love can become so immense, God warned us to not let them (our family and children) distract us from His remembrance.

Parents can do unimaginable things out of love for their young ones. And you need to experience it first hand to truly understand it. Mothers put their lives at risk whenever they give birth to a child. But what happens after that? Despite all the pain and suffering through labor, the mother is overflowed with joy and happiness, so much so that the sight of the baby subdues the pain.

Fathers may not have the same unreal experience. They may not have as much compassion towards the child as the mother. But still, his love to his children will still be intense. And to be separated from the children, and family in general, is an unpleasant experience. And I say this from real life experience.

It would be most ideal if we could be together with the ones that we love forever and ever. But even in the best condition, it will never happen in this worldly life. There will always be the chance to be separated, whether because of job needs, school, business, and of course death.

However, there is one way to be gathered together FOREVER, in the best of places, as mentioned in the Qur’an. What we need to do is to believe and commit ourselves to good deeds. Furthermore, we also need to educate our children so that they do the same. In turn, they will do the same to their children and them to theirs, and it goes on and on until the end of time (by God’s will).

By doing so, we will be brought back together in eternal bliss. And the best part is, not only will we be gathered by our children, but also with our grandchildren, our great grandchildren, and so forth.

Thursday, July 19, 2012

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 no 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

Wednesday, July 18, 2012

All of us will whither in the end…

It’s summer time here in Japan. Although hot, the plants are at their full lushness (it’s around 34 degrees here in Kyoto, and it will get hotter in August). It’s hard to imagine that just a few months ago, at the end of winter, all of these plants didn't even exist. Well, they might have existed as roots, being dormant, as seeds ready to germinate or whatever, but to the naked eye, they were literally, dead.

The weather changed, spring came, and suddenly all these plants just came out of nowhere. Showing their beautiful spring colors. The sakura (cherry blossom) flowers bloomed, the tulips bloomed, the ume (plum) flowers bloomed, along with all the other amazing flowers and plants. Everybody loves spring, photographers particularly. They can get amazing shots that would have been impossible to get in other seasons.

But all this beauty and magnificence, they don't last very long. Cherry blossoms (which is often used to symbolize Japan) are in full bloom for only two weeks at maximum. If rain comes, their display of beauty could end even sooner. And that goes the same for other flowers as well. In fact, even though the trees and plants are at their full lushness right now, in another few months, they will eventually wither and “die” all over again.  

Such is a lesson for all of us. Nothing lasts forever. It’s a cycle of creative magnificence. Just as we were brought into this world as babies, grew strong and beautiful, full of “lushness”, we will also wither and come to our time eventually. Some of us won’t even be given the chance to reach old age. So it is not so far fetched if we were to be raised up again, even if it’s as a new creation all together. Isn’t it easy for The One who created us in the beginning?

Friday, July 13, 2012

The disappearance of religiosity

Not very long ago people used to be religious. They used to hold on to religion and make it their life rope. Their lives revolved around religion. Constitutions of countries were based on articles of faith. Not many people denied God nor questioned whether God exists or not, because for them, the answer was obvious. In fact, I just saw a video of Magic Johnson when he gave a speech on behalf of the US basketball dream team, and the first thing that he mentioned was God. Similar to Hakeem Olajuwon when he was admitted into the NBA hall of fame, where the first thing he said was “I thank God.” I believe that we wouldn’t hear that kind of opening from this generation of NBA players.

Look at how degraded we have become. The quality of our religiosity and the religiosity of the society has dropped so far that it has come to the point where many don’t even want to admit/believe in God. Nowadays, by rejecting God, people feel as if they’re cool, smart, and liberated. Feeling a false sense of superiority, believing that they’re modern thinkers, thinking ahead of others. Of course we are free to think what we want to think. But feeling superior because of not believing in God is absurd.

The root of the drop in religiosity is perhaps ignorance (which leads to concluding things with inadequate amount of knowledge), greed, and arrogance (which results in rejecting the truth even if he has inclination towards it).

Nevertheless, God is Merciful and opens some doors of guidance to us from time to time. He gives us opportunities to “snap out of it” at certain periods. These opportunities might come through spiritual experiences, interaction with pious people, or maybe through shock therapies that He gives us.

One story about this is eloquently told in the Qur’an. Although I am paraphrasing, I hope that I don't distort it.

There were people that owned a productive and beautiful garden. They benefited from the garden very much and had overwhelming confidence in their skills. They eventually shifted their mindset from attributing their success to God, to attributing their success to themselves and their garden. This mistaken way of thinking is a result of ignorance and arrogance blended together. Forgetting the true nature of things (that God is the one who gives success) and feeling self-sufficient, not needing God. They also developed a selfish attitude, wanting to have all the harvest to themselves without giving any portion to charity. They had a drop in their religiosity.

But then God, being merciful as He is, reminded them through shock therapy. Just as they were about to harvest their crops, they found their garden burnt to ashes. Through this, they “snapped out of it” and realized their mistake in being ignorant, arrogant, and selfish (greedy).

The disappearance of religiosity is most probably attributed to the mentioned traits. We are indoctrinated that success is the fruit of our effort only and that we are entitled to enjoy it alone without sharing it with others.

When we wake up, prepare for work, how many times do we direct our intentions for serving God? When we look at our career and our successes, how many times do we thank God and see it as a blessing that He has blessed upon us? When we receive our monthly payroll, how often do we think about giving a portion of it to charity? If the answer is in the negative, we should try to get back on track and not make the same mistakes of the people of the garden, lest lose our religiosity and share the same destiny.