Night and day, a sign for the mindful

The normal cycle of a human being is to sleep/rest at night and work in the day. Scientifically, the phenomenon of the body’s cycle is explained by a term called the circadian rhythm, which was made popular by scientists in the early 20th century. It means an approximate daily periodicity, a roughly-24-hour cycle in the biochemical, physiological or behavioral processes of living beings, including human beings. In simple words, what our body is supposed to do (rest or be active) at a given time.

The main factor that affects the circadian rhythm is the light accepted by a region in the brain (hypothalamus). However, the light that affects the circadian rhythm is highly specific (in wave length, intensity, and other attributes), and to no surprise, the corresponding attributes are found in no other than our own sun.

Allah the Almighty has said about this in The Qur’an in Surah (chapter) Yunuus verse 67:

Which can be approximately translated (according to Tafseer Al Jalalayn) as

“He it is Who made for you the night that you should rest therein, and the day to see. Surely in those are signs, indications of His Oneness, exalted be He, for folk who are able to hear (those who think deeply).”

Allah the Almighty has made it clear for us to use the night to rest, and the day to “see”. The word “see” here shows Allah’s define knowledge (revealed to our beloved Prophet nearly 1400 years ago) that it is indeed “light” that affects our cycle, similar to what has only been recently discovered using modern science. Note the precise manner in which Allah addressed this matter. 

The amazing transition of night to day

In my laboratory here in Japan, everyone works on an average of more than 10 hours a day. Some from 8 a.m. to 11 p.m., some work shorter but there aren’t a few who work even longer. However, the majority stay disciplined and use the night for resting. This normal cycle doesn’t apply for everyone though, as there are some who prefer to work at night and sleep in the day. This actually reminds me of what I used to do in my undergraduate years, where I participated in events that sometimes went on until morning. At those times, I’d sleep in the morning, and get up at noon. To me, it felt terrible. I’d feel unfit and would need to chase things the whole day to adjust myself to the normal cycle of people around me.

Straying away from what’s natural (of what Allah has commanded), can lead to serious disorders. In the case of disregarding the natural cycle of night and day, one can experience disorders such as the circadian sleep disorder (results in insomnia or excessive sleepiness during the day), the delayed sleep phase syndrome (could only sleep after 2am), and others. 

There are so many phenomena around us that we overlook (and consider casual) due to our ignorance. The alteration of night and day is one of them. How the earth precisely rotates, how the distance between the earth and the sun stays that way, our body’s the circadian rhythm, and everything we can think of, are all proofs of the perfection in His creations. If we ponder and think about the creations, it will further increase our faith and belief in the Almighty creator.

Approximate meaning (Yusuf Ali translation):

“Behold! in the creation of the heavens and the earth, and the alternation of night and day, there are indeed Signs for men of understanding (Ali Imran 190)”

May we all be given the awareness and wisdom to ponder on all the blessings that Allah has given to us, no matter how “small” or “casual” they may seem.

Keywords: circadian rhythm, science, scientific, Ali Imran 190, Yunuus 67, night, day, Qur'an

Rivalry in achieving false success

In our so called modern civilization, almost in all societies, success and happiness is measured with how secure someone is financially. Even school and education are directed towards being “financially secure”, where the end product is to be able to gain a good job with a high paid salary. This of course ruins the true purpose of why one should receive education in the first place. When someone has a large paycheck and trillions of currency in their bank, people will unanimously say that he/she is successful.

The quest to achieve this kind of success has become a rivalry among people. People compete with each other to be most “successful” disregarding all the consequences. People compete with each other to get the highest pleasure/joy this world has to offer by buying all the luxurious things that they can buy. Beautiful clothes, big houses, exotic cars, antique glassware, Rolex watches, the highest/most expensive education, and everything else that can make them look the most “successful”.

The traps seducing us to drag ourselves to adopt the same attitude (to reach for this kind of success) is empowered by almost everything around us. Everywhere we look, there are always temptations. We’re seduced by the soap operas on the TV, the ads and articles about these “successful people” in magazines, the billboards using these “successful people” as if they are heroes, etc. For Muslims, this is something we need to beware of, as it’s one of satan’s trick to misguide the majority of humanity.

Devine words from Allah in the Quran has stated the danger of getting carried away in the rivalry to gain this kind of false success, including the piling up of riches, in Suraah (chapter) At Takaathur.

This has approximate meaning (according to Yusuf Ali’s translation) as the following:

1. The mutual rivalry for piling up (the good things of this world) diverts you (from the more serious things/obedience to Allah),

2. Until you visit the graves.

3. But nay, you soon shall know (the reality).

4. Again, you soon shall know!

5. Nay, were you to know with certainty of mind, (you would beware!)

6. You shall certainly see Hell-Fire!

7. Again, you shall see it with certainty of sight!

8. Then, shall you be questioned that Day about the joy (you indulged in!).

For Muslims, the surah is a serious warning about being indulged in the competition and rivalry to enjoy the joys of this world. In this surah, Allah repeatedly reminds us (emphasizing) on the danger of striving to achieve the “false successes” that this world has to offer. This warning is not on things that are forbidden (haram), but rather on the halal things, which have the potency to make us forget about our real purpose (which is to worship Allah and do righteous deeds). If the basis of all that we work for is only to achieve this kind of false success, we will indeed be the losers in the end. Everyone, even the ones who have doubt will be certain about this matter at the time their dead bodies are taken to the graves, the moment where their short lives end.

True success cannot be achieved through collecting riches. It can never be achieved, as it is in human's nature to never be satisfied and always want better things than what he owns. True success can only be achieved when a human being bases his actions on what he/she is supposed to do, which is to do righteous deeds and prevent evil. This world is full of traps and tricks that attempt to corrupt our true nature (as noble beings), and that is why we all need to equip ourselves to protect our nobility.

May Allah protect us all from all the evil that this world has to offer.

Keywords: At takaathur, human nature, Satan, life, rich, poor, islam, happiness, success

The Cost of Arrogance

There's arrogance in all of us. We were created that way, so it's in our nature and it'll never change. However, some can control their arrogance and some cannot. Most people, including myself, fall into the second category, the ones who have a hard time controlling their arrogance.

The cost of letting our arrogance take control can sometimes be devastating. It can ruin friendships, destroy marriages, lead into war and killings, and worse, it can inflict the wrath of the All Mighty. An arrogant person will often hurt his/her friends feelings, an arrogant husband who disregards his wife will be the source of a bad marriage, the arrogance of Hitler lead to the massacre of millions of Jews in World War 2, and the arrogance of Satan who refused to bow to Adam lead to the wrath of Allah The All Mighty.

The arrogance of Satan is the worst. Because he knew that he was facing The Sustainer of All Things, The Most Knowledgable of All, yet he still maintained his arrogance and disobeyed. This event is recorded in the Holy Qur'an in Al Hijr verse 31-43


which has approximate meaning:
31: Not so Iblis: he refused to be among those who prostrated themselves.
32: (Allah) said: "O Iblis! what is your reason for not being among those who prostrated themselves?"
33: (Iblis) said: "I am not one to prostrate myself to man, whom Thou didst create from sounding clay, from mud moulded into shape."
34: (Allah) said: "Then get thee out from here; for thou art rejected, accursed.
35: "And the curse shall be on thee till the day of Judgment."
36: (Iblis) said: "O my Lord! give me then respite till the Day the (dead) are raised."
37: (Allah) said: "Respite is granted thee
38: "Till the Day of the Time appointed."
39: (Iblis) said: "O my Lord! because Thou hast put me in the wrong, I will make (wrong) fair-seeming to them on the earth, and I will put them all in the wrong,-
40: "Except Thy servants among them, sincere and purified (by Thy Grace)."
41: (Allah) said: "This (way of My sincere servants) is indeed a way that leads straight to Me.
42: "For over My servants no authority shalt thou have, except such as put themselves in the wrong and follow thee."
43: And verily, Hell is the promised abode for them all!

By the order of Allah, all creatures but Satan bowed to Adam, the first human being. Satan's arguments were based upon the nature of his creation (fire) versus the nature of Adam’s creation (soil/clay). This inflicted the wrath of Allah, and Satan was cursed for eternity. His one promise was to do his best to misguide all of Adam's descendants but a few. The only ones who can avoid Satan's misguidance are the ones who uphold justice and perform good deeds.

Satan's arrogant view on who is more superior is a materialistic view which is actually already widespread and common in our civilization, where one is deemed superior based upon ones ancestral background, nationality, race, richness, etc. This is a view that we need to eradicate if we truly want to uphold equity and justice throughout the human race. Islam teaches us that human beings only differ according to the good they bring for other people.

Arrogance is a dangerous attitude, and it will eventually destroy the person who commits it. The common sense is that arrogant people should have few or no friends. Unfortunately in real life, we often find that people with the most arrogant attitude are the ones who are most popular and liked. The civilization we live in has already become so twisted and has been turned upside down, that many things contradict common sense. I guess Satan has succeeded in his promise to misguide all of Adam's offspring and descendants but only a few.

May we be able to avoid, or at least control our arrogance and be among the guided ones…

keywords: al hijr, 31-43, satan, human nature

Our greed for this world

There is no doubt that all human beings have the potential to be greedy. When someone follows his/her desires without any other consideration, there is a big chance that they develop their “greed” potential to blossom. Unfortunately, the “coca cola civilization” we currently live in is based on the fulfillment of satisfying desires. Among the products of the civilization, seeking for riches and financial security has become a way of life.

Of course we were MADE to think that riches and financial security can bring us joy, happiness and comfort. This view is only partially true, as it only gives temporary happiness. To maintain this false happiness, one will want to gain more and more, even when he/she doesn’t need it, in order to fulfill lust and desire.

Many will disagree that these so called “rich” people are greedy and they have worked hard for their success. But the facts suggest otherwise. Look at the newest list of the “Top 10 Richest People of the World” from Forbes magazine. In that list, we will find that four people in that list are Indians, the rest are a mix of countries from four different continents.

What’s shocking is that despite contributing up to four people to the list, in India, 45% are living in poverty (according to World Bank’s definition of poverty=people living with less than 2 USD per day). This is a sad fact, because each of these “rich” people have a net fortune of more than 20 billion USD, which is almost enough to feed all the poor people in the world (3 billion people), for one day at least. And with their running businesses, it wouldn’t be hard for them to regain the fortune they have in no time. However, their greed has forbid them from spending most of what they have in charity.

Islam emphasizes that this current life of ours is only temporary, and everything that we own (including our wealth) is only trusted to us from God for the benefit of others. What we truly own is what we give for the benefit of others. Nevertheless, there have and always will be people who are greedy for life. Ones whose hearts are so attached to this world, that it makes them ignorant towards all the suffering around them. The Qur'an describes this situation in Al Baqarah verse 96:


The approximate meaning is:
“And thou wilt find them greediest of mankind for life and (greedier) than the idolaters. (Each) one of them would like to be allowed to live for a thousand years. And to live (a thousand years) would by no means remove him from the doom. Allah is Seer of what they do.”

The verse talks about a group of Jews at the time of the Prophet (saw). They enjoyed life so much that they became greedy and wanted to live for 1000 years to be able to enjoy the wealth, power, and everything that can fulfill their desires. However, as stated before, this life is but temporary, and everyone is destined to die and be taken account for what he/she did in life, good or bad. And at that time, whosoever did bad will taste the payment (doom) for what he did.

Greed is one of the major obstacles to eradicate poverty. If everyone had the consciousness to give in the sake of caring for other people rather than buying something that he/she doesn’t really need, poverty wouldn’t even exist. Islam offers the path towards this. Too bad not even the best Muslims (which are quite a few nowadays) can totally get rid of their desire/greed for this world. May we all be given the power to detach our extensive love towards our wealth and desires.

Keywords: Al Baqarah, 96, wealth, poverty, fortune, richness, world

Banking interests = rejecting blessing

Bank interest is one of the major features of conventional banking. Be it an investor, a loaner, or a depositor, everyone will receive or pay interest. In the case of deposits, one will receive an added amount of money without any effort. And in the case of borrowing, one must pay a certain amount, surplus to what he/she has borrowed.

People borrow money from modern banks for many purposes, from starting a business to buying a house. Even third world countries borrow from banks/or institutions such as the Asian Development Bank (ADB) and the International Monetary Fund (IMF). In many cases, the borrowers spend most of their lifetime and efforts to pay off the interest rather than paying the real loan.

Islam clearly prohibits interests in any form. Interest or riba or usury is said to bring more corruption than goodness, Islam prefers charity and fair trade, as mentioned in the Quran, surah Al Baqarah verse 276:

Which has approximate meaning:
“Allah will deprive usury of all blessing, but will give increase for deeds of charity: For He loveth not creatures ungrateful and wicked.”

Interests in Islam are viewed to be wicked and cruel. It also erases the blessings that our riches bring to us. Everything we buy which includes the usage of that interest is also deprived of His blessings. Charity and lending money out of good intention is valued as a much better option in Islam.

Unfortunately, even in majorly populated Muslim countries, the so called modern banking system that promotes interest (riba/usury) is still very much dominant. The top banks in Arab are dominated by semi conventional banks such as the National Commercial Bank and Al Rajhi. In Indonesia, the top banks are conventional banks such as Mandiri and Central Bank of Asia (BCA). Nowadays, there are even some banks who claim to take no interest (following the Islamic way), yet only change “interest” into something less intimidating for Muslims such as “benefit”. There is a glimpse of hope though, as there are several Shariah banks (Banks based on Islamic law) which are steadily growing, such as Shariah Mandiri in Indonesia.

I am no economy expert and am unable to dive deeper into the technical differences of conventional and Islamic banking. But the use of no interest is beginning to be partially implemented in several countries such as Japan. In Japan, deposits are not given any interest (0 interest rate), even though loans are still subjected to interest.

The persistency of using the services of these conventional banks might be one of the causes why these Muslim populated countries are in such a bad mess. When the guidance from the Quran and Hadeeth are neglected, Muslims should beware and introspect on all the misery that is given upon them.

May we all be people who have the heart to give in charity and kindness.

Keywords: interest, banking, bank, Islam, Shariah, riba, usury, al baqarah, 276

People Who Challenge and Change Nature

Humans are given free will by God. Choices are ours to take.

This is also true in regard to our attitude towards nature. We have the choice to tamper with nature and adjust it according to our will, and destroying it through our greed or we can cherish it and wisely benefit from it. It seems that our civilization is opting for the first option, which I don’t think is a very wise choice.

We change things in nature to what we think is best for us with our limited knowledge. We tamper with genetic attributes of organisms for our economical benefit, not knowing what the consequences are. We change our appearances through plastic surgery to be more attractive to others (did you know that there were 11.7 million cosmetic procedures in the US in 2006?). We create artificial rain to fill up dams not knowing what effect it may have on global climate. We kill animals that seem dangerous and not beneficial with little or no knowledge about them.

Humans have a tendency to want to take control of everything which is of interest. Unfortunately, we severely lack the knowledge we need to be able to tamper with the ways of nature. Muslims are ordered to think about Allah’s creation, but for goal of understanding it, and realize the Creator’s greatness. However, muslims are ordered to be very careful in utilizing the creations (nature). In fact, the Quran has warned the danger of following the people that change nature. As said in Al Maidah verse 119,


The approximate meaning (Picktall’s translation):

"And surely I will lead them astray, and surely I will arouse desires in them, and surely I will command them and they will cut the cattle's ears, and surely I will command them and they will change Allah's creation. Whoso chooses Satan for a patron instead of Allah is verily a loser and his loss is manifest.”

The verse talks about the disbelievers, which take Satan as their helper. They also walk the path that Satan has built to misguide humanity, giving them false hopes and delusions of grandeur. Allah is the One Who permits this to happen, and verily it is He who knows best. One of their main characteristics is that they will change the nature of Allah’s creation to what they think is better.

Every creation has its purpose, no matter how bad or ugly it may seem for us. Take cockroaches for example. It might be a bit difficult to find anything positive related to this insect. We always relate it to trash, disgusting, and other filthy words. However, cockroaches can serve as bio-control agents in agriculture, to control lepidopteron pests such as moths and butterflies. The ugliest person in our eyes might be the kindest of all, which is what really counts. We should never judge Allah’s creations to be good or bad using our simple and incapable minds, more else change them into what we think is better.

May we all be protected from false hopes and dreams, and be among the righteous.

Keywords: genetic modification, an nisa, 119, greed, Satan, Nature, Choices

Emigrating To avoid oppression

The word emigration means moving out from one place to another. Nowadays, emigration from one country to another country is very casual. As a matter of fact, for mostly economic reasons, more than 400.000 Britons have emigrated from Britain since 2006. Another example is the emigration of Carpe Varde citizens to the US due to the hardships they face there.

The reasons for people to emigrate may vary from economy, chances of studying, following a spouse, to avoiding oppression. I'd like to emphasize on the last reason, which is to avoid oppression. Many people in many countries have to comprehend with the oppression they receive, either from their own people, or from invading countries. We can find many kinds of oppressions. Some might not even realize that they are oppressed.

In Indonesia for example, oppression is an everyday meal. The rich oppress the poor, the poor oppress the poorer, the strong oppress the weak, and the weak oppress the weaker. This use to only be the case in big cities such as Jakarta, but nowadays it is beginning to become widespread. There is not much to do though, as the media helps spread and mold this situation. It oppresses the mind of Indonesians through continuous nonsense promoting oppression of others (such as useless comedy, mystisism, gossips, entertainment, violence, etc), for their own financial benefits and ideologies. And the worst part is that people can't get enough of it.

Anyway, there are times when people try to fight oppression, but cannot overpower it due to its overwhelming dominance. At this point, the best option is to retreat, and emigrate to find a better place to uphold justice, at least to a place where there is no oppression towards them.

This is also the case in Islam, as Allah has said in the Qur'an, Surah An-Nisa verse 97-100. The verses say that people who are in the state of wronging themselves (when death reaches them) due to the influence/oppression of their society will be among the ones who are in ultimate misfortune. There is exception to this, which is for those who are weak and do not have the knowledge to devise a plan to emigrate by themselves.

Emigrating in the name of Allah in order to seek justice is praised and is a good deed in Islam. Even Prophet Muhammad had to emigrate from Makkah his home city, to Madina, after his people oppressed and drove him away. But then he came back after building the strength of the Muslims to uphold justice and bring goodness to the city. The Prophet's situation somehow mimic the condition that Muslims face today, especially in the west. Where many Muslims are oppressed, taunted and stripped of their freedom to implement their beliefs.

Emigrating should always be looked as a choice when we feel that we can do more good at another place. Whether if it is to emigrate to a new village, a new city, a new province, or even a new country. We should be strong at heart and head and try to let go of the ties which we call home, nation, etc. All of that is on the earth actually belongs to God, and it is for us to manage and benefit from.

keywords: An nisa 97 98 99 100 emigration hijrah oppression islam

“Peacekeepers”, the ones who spread mischief and corruption

“…. I'm optimistic because I have faith in freedom's power to lift up all of God's children, and lead this world to a future of peace….”

The above is a quote from a speech given by the President of the US, George W. Bush for the National Republican Convention on the 2nd of September 2008. The speech was delivered as advertisement and endorsement for John McCain as the Republican candidate for the upcoming US President election. The speech is by no means bad, and the US President has delivered many similar speeches, emphasizing in peace, justice and order.

Ironically, contrary to all the speeches on peace, justice, and all sorts of utopia, in the last decade, it is the US who has committed crimes against humanity, invading other country’s territory, and killing thousands of civilians along the way. Even worse, these so called “war against terror” in Afghanistan (2001) and Iraq (2002) were also based on a bunch of lies (no weapons of mass destruction, and no Osama bin Laden capture). There are also immoral conducts reported to be done by the US military there.

For the aftermath, things have even turned for the worse. John Pilger made a documentary in 2004 called “Breaking the Silence”, which gives us an alternative view (from the mainstream media) of what has/is really happening in Afghanistan and Iraq. Regarding Afghanistan he mentioned that “No country has been this devastated since Polpot’s Cambodia.” Besides the invasions, there are also secret operations to interfere with other country’s affairs, especially third world countries in Asia and South America.

In every civilization there will always be people, who claim to be the just, peacekeepers, yet have large contribution towards destruction (physical and moral). It is because peace is not the final goal, rather a jargon to reach what they really want (e.g. wealth, power, stability, comfort). There are also these kinds of people in Prophet Muhammad’s (saw) time, as written in the Qur’an in Surah Al Baqarah verse 11-12:

(2:11)
وَإِذَا قِيلَ لَهُمْ لاَ تُفْسِدُواْ فِي الأَرْضِ قَالُواْ إِنَّمَا نَحْنُ مُصْلِحُونَ

(2:12)
أَلا إِنَّهُمْ هُمُ الْمُفْسِدُونَ وَلَـكِن لاَّ يَشْعُرُونَ

The approximate meaning are:
2:11 When it is said to them: "Make not mischief on the earth," they say: "Why, we only Want to make peace!"
2:12 Of a surety, they are the ones who make mischief, but they realize (it) not.

They are the hypocrites who act noble and just in front of people, yet scheme while nobody is looking. They are the ones who spread mischief and corruption. A further verse says that Allah will let their corruption and mischief continue, and even intensify them so that they become lost in their lust and greed (Al Baqarah verse 15).

Those are the words of God, and there are no words truer than that. If we try to contemplate and think deeper (with good prejudice) towards what has been happening lately, these verses mean a lot. May all of us be the ones who are guided on the right path…

Keywords: US, Iraq, Afghanistan, war against terror, mischief, corruption, al baqarah 11 12 15

Heart Hardness

There are some people who defy truth, and do not want to comply with anything but his/her own desires and lust. This is what we call having a hardened heart. It is one of the most dangerous attitudes, because it will lead to ignorance, the cease of learning and thinking rationally. In many cases, we might also experience glimpses of it, where our common sense and judgment are defeated by our desires.

For a Muslim, the hardening of the heart is one of the most feared punishments from Allah swt, which is the result of continuously disobeying Him. In fact, it is so dangerous that it is mentioned many times in the Holy Quran. A quick search using Islamicity’s Qur’an search resulted in 8 hits.

Unfortunately, I have a feeling that many people are already given this punishment due to how they live their lives. Many of us tend to get carried away by the flow of our modern life, develop ignorance, and unconsciously disobey Allah swt. The worst case is illustrated in Surah Al Baqarah verse 74, which provides warning for me and all of us as well. 

ثُمَّ قَسَتْ قُلُوبُكُم مِّن بَعْدِ ذَلِكَ فَهِيَ كَالْحِجَارَةِ أَوْ أَشَدُّ قَسْوَةً وَإِنَّ مِنَ الْحِجَارَةِ لَمَا يَتَفَجَّرُ مِنْهُ الأَنْهَارُ وَإِنَّ مِنْهَا لَمَا يَشَّقَّقُ فَيَخْرُجُ مِنْهُ الْمَاء وَإِنَّ مِنْهَا لَمَا يَهْبِطُ مِنْ خَشْيَةِ اللّهِ وَمَا اللّهُ بِغَافِلٍ عَمَّا تَعْمَلُونَ 

The approximate meaning of the verse is:

“2:74 Thenceforth were your hearts hardened: They became like a rock and even worse in hardness. For among rocks there are some from which rivers gush forth; others there are which when split asunder send forth water; and others which sink for fear of Allah. And Allah is not unmindful of what ye do.”

The verse illustrates the disobedience and denial from Moses’ people, whom after being given miracles over and over, kept looking away from the truth. Their hearts are illustrated to be harder that rocks. Rocks however, are breakable. Constant water flow can carve rocks through erosion, which is unlike the hearts of those who deny after given clear proof.

I believe that with strong effort, our hearts can be purified again. Through total submission we will be able to gain true tranquility in our hearts. This however, can only be achieved with sufficient knowledge on what the right path is, and there is no better time to increase our effort to learn than in Ramadhan. I hope we all strive to find ultimate truth, and be among those whom hearts are pure.

Keywords: Heart Hard Islam Al Quran Al Baqarah 74

Our wealth and justice

Most people around the world have a dream, where you’ll be sufficient and happy by earning enough money to enjoy life and keep you financially secure for the rest of your life, very much influenced by the “American dream” really. This point of view affects almost every aspect of life, including how we comprehend justice. Although more and more people are beginning to be aware with our misperception of justice, let’s face it, most are seeing justice from the eyes of the powerful and rich (where the weak and poor are non-factors and dispensable).

As long as the rich are frightened to lose their wealth, and the poor struggle to stay alive, justice will always remain untrue and discriminative. At least that is what’s happening right now in my home country, Indonesia (and in many third world countries I believe). The corrupts run loose and enjoy their loot because they can afford to, while petty thieves (that often need to steal to stay alive) are often beaten to death. The rich become richer and more comfortable, while the poor become poorer and more miserable. No justice there I feel. And how often do we stand still when someone steps all over the justice we believe in?

True justice is somewhere hidden inside our hearts, covered by our interests, lust, and greed. We need to shred those individual interests, lust and greed away, in order to see and be brave to uphold true justice. For a Muslim, the best way to shred individual interest is to fully commit him/herself towards God’s sake. Unfortunately, although many people are said to be Muslims, they aren’t putting enough effort to understanding Islam and act upon the teachings.

Purifying our hearts
Islam teaches us NOT to put wealth in our heart, because wealth corrupts the heart, it will surely be exhausted (one way or another) and cannot be of any true help to us in the face of calamity, as presented in the holy Qur’an (Al Kahf verse 32-44). Wealth should not become an obsession or goal, yet should only be used as a tool to reach blessing (by helping the poor, supporting orphans, etc.). By not putting wealth in our heart, we will be able to have clearer perception on things, including our perception towards justice.

Muslims are explicitly ordered to uphold justice. If there are any Muslims doing the opposite, then they have deliberately disobeyed Allah. As said in the Quran in An-Nahl verse 90, the verse has approximate meaning:

“Allah commands justice, the doing of good, and liberality to kith and kin, and He forbids all shameful deeds, and injustice and rebellion: He instructs you, that ye may receive admonition.”

The verse is very clear, direct and easy to understand. Islam brings human beings back to fitrah, our natural state, so everything in Islam should be natural for us (=easy to do).

As I have mentioned, our incapability to see justice is because it is covered up by our interests, lust and greed to what is offered by this world of ours. Everybody, no matter how corrupt, are built by Allah to have justice in their hearts. I know I have simplified many things in this post, and the problem is probably more complex. But I believe that our lust and greed is one of the main culprits. And for a Muslim, the reasons above are more than enough reason to be brave in upholding justice.

Keywords: An Nahl verse 90, Al Kahf verse 32-44, justice

Our most dearest

As human beings, we have a tendency to care about the things that we own or have. Be it our parents, our family, our career, our wealth, and everything else we have. It’s perfectly OK for us to care for them. However, the things we care about sometimes interfere with what we believe in. For a Muslim, there is a possibility that our care and love inhibits us in fulfilling our destiny to be Allah’s Khalifa (leader) on earth, to be blessings for the universe. In another word, our love for other things competes with our ultimate love for Allah.

How many times have you sacrificed what you believe is right for the sake of your family, your career, for increasing your wealth, or other things? Although all of them may correlate and can be synergized, there are times when we have to choose our priority. One example is to walk a path/career which is forced on to you by other people. For a Muslim, he/she is supposed to pray at the beginning of the praying time, which is the best time to pray. But our business often makes us postpone it until the last minutes. Be it our work, our travel, or even merely chatting with friends. There are even times when some of us are “forced” to combine prayers (jama) when we actually don’t need to, or even forget it completely.

Allah has given a warning in the holy Quran about this through surah At Taubah verse 24 about this.

قُلْ إِن كَانَ آبَاؤُكُمْ وَأَبْنَآؤُكُمْ وَإِخْوَانُكُمْ وَأَزْوَاجُكُمْ وَعَشِيرَتُكُمْ وَأَمْوَالٌ اقْتَرَفْتُمُوهَا وَتِجَارَةٌ تَخْشَوْنَ كَسَادَهَا وَمَسَاكِنُ تَرْضَوْنَهَا أَحَبَّ إِلَيْكُم مِّنَ اللّهِ وَرَسُولِهِ وَجِهَادٍ فِي سَبِيلِهِ فَتَرَبَّصُواْ حَتَّى يَأْتِيَ اللّهُ بِأَمْرِهِ وَاللّهُ لاَ يَهْدِي الْقَوْمَ الْفَاسِقِينَ

The approximate meaning is:
“Say: If your fathers, your sons, your brothers, your wives, your kindred, the wealth that you have gained, the commerce in which ye fear a decline, or the dwellings in which you delight are dearer to you than Allah, or His Prophet, or the striving in His cause, then wait until Allah brings about His decision. And God guides not the rebellious.”

This warning should not be taken lightly. As I am very sure that many Muslims, including myself, often put a lot of things in priority above obeying Allah’s commands, things that often have nothing to do with striving in Allah’s cause. However we love something, it should not distance us from Our Lord. And to uphold Islam, this bad habit has to change…

So what IS dearest to you?

Many of us may not read the Qur'an that often, or even if we do, we don't understand the meaning. It is what is causing Islam's decay. People walking around saying that they are Muslims without knowing what it truly is. It has to change. Read it bit by bit, and you will definitely find many interesting things that you never thought you'd find. May all of us be able to fulfill our destiny of becoming Allah’s Khalifah through love and total devotion towards Allah.

Keywords: At taubah 24, Islam, religion, quran, holy, qur'an, love

Being Imprisoned...

"The one who is (truly) imprisoned is the one whose heart is imprisoned from Allah, and the captivated one is the one whose desires have enslaved him."
-Ibn Taymiyyah-

I'm imprisoned
by school,
by culture,
by photography,
by football,
by the internet,
by technology,
by songs,
by Hollywood,
by delicious food,
by the NBA,
by sports,
by fun,
by money,
by desires,
by life...

The things I think I like and love
Are actually a web of traps
Wasteful things
To eat up my time, my soul and make me lose my way
Distorts me from being noble, righteous and free

Freedom is just a few rejections and steps ahead
With a hard head and hard heart,
Let us conquer life, rather than be conquered by it!!

Facing the enemy's deceits

Enemies are real. They don't only show up in fictional cartoons, movies, or books. They are real, even though sometimes we don't know who or where they are. It can be the most unexpected person. It can even be your co-worker trying to make his/her way to the top (and thinks that you are an obstacle).

Well, I believe that no matter how good a person we are, we are bound to make enemies in some point of our lives. The Qur'an also informs us that even the prophets of monotheism had their enemies. Yusuf (Joseph) a.s. had to face his jealous brothers and the deceits of his master's wife (when he was a slave), Moses a.s. had to face the not mighty pharaoh, Isa (Jesus) a.s. had to face the Jewish rulers and priests, and Muhammad s.a.w. had to face the Quraish leaders (and even now after his death he still has to face many forms of enemies).

One of the assault weapons that people use nowadays are lies and deceits. The war happens in the media. The art on how to create and direct opinions of the public. The prophet Muhammad (and Islam literally) has recently been battered by several media games (the cartoons by jylland-posten in the name of free speech, the "fitna" movie by Geert Wilders, and other forms of mockery), which was responded inelegantly by most of the Islamic community by doing disrespectful actions (by burning flags, vandalism, etc).

I know everyone is upset and angry, but how should we respond?

According to surah Al An'aam (112), insults, mockery, lies towards Islam is by Allah's will.

Here's the 'aayah:
وَكَذَلِكَ جَعَلْنَا لِكُلِّ نِبِيٍّ عَدُوًّا شَيَاطِينَ الإِنسِ وَالْجِنِّ يُوحِي بَعْضُهُمْ إِلَى بَعْضٍ زُخْرُفَ الْقَوْلِ غُرُورًا وَلَوْ شَاء رَبُّكَ مَا فَعَلُوهُ فَذَرْهُمْ وَمَا يَفْتَرُونَ

The approximate meaning is:
And thus it is that against every prophet We have set up as enemies the evil forces from among humans as well as from among invisible beings that whisper unto one another glittering half-truths meant to delude the mind. But they could not do this unless thy Sustainer had so willed: stand, therefore, aloof from them and from all their false imagery!

He, The Almighty has promised it in the Qur'an, and has also given us instruction on what to do. The best respond is to not make it a big deal. We should counter it by straightening the misunderstanding, say that it's wrong, and just move on and continue being good muslims. If we get eaten up with the issue and overreact, we have successfully fallen into their trap...

May we all be given the power to stay poised and patient in facing all our enemies...

Keywords: Muhammad Mohammed Mohamed Cartoon Danish Newspaper Quran Terrorism Islam al an'aam al anaam 112

Our insignificant knowledge

Human beings are curious creatures. We try our best to understand what we don't understand, and do a pretty good job in doing so. We've came a long way since the beginning of history. From only knowing how to use modified rocks, to being able to understand and utilize complex matters such as chemical compounds, microbes, genes, and nano-materials. Without doubt, science plays a very strong part in our current way of life. As through it we are able to enjoy the luxury of the things we currently enjoy, such as electricity, internet, soap, and gazillions of others that are too much to mention.

Humans were destined to be great. We are the only creatures that can build and use our knowledge for our benefits. It gives us the potency to be most noble among all of God's creatures. There are thousands of scientific papers and articles that report new findings at a daily basis (which also shows that there is still much to learn). However, our overwhelming knowledge can be too much to handle sometimes. As it can often make us over confident and even worse, arrogant. It makes us think that we can control and solve EVERYTHING. Acting as god... We tend to be ignorant that all the knowledge that humanity has gained, is actually insignificant to what is NOT known... Like a drop of water in the big blue ocean.

One of the ultimate questions that is yet to be solved by science is the mystery of life and death. Nobody can predict when someone is going to die, how the process is, and so on. And nobody can predict the exact time a baby will be born. The matter is beyond our knowledge and science, and I believe that it is a secret that only God knows. Besides life and death, there are many questions that humanity is still baffled about. The entity of time, the magnitude of the universe, the work of the brain, are just several among the unsolved questions we have.

Furthermore, our knowledge is also prone to mistakes. An article in newscientist published in 2005 describes that most reports in scientific papers are wrong. Claiming that there is less than a 50% chance that the results of any randomly chosen scientific paper are true (it probably also applies for the article itself). Which is astonishing, as the scientific community and the papers they publish represent the front liners of scientific development, and science itself.

The wrap up is that our science and knowledge is limited, insignificant, and prone to mistakes. So we should stop being arrogant, and accept that we have our limits (but it doesn't mean we can stop learning! Just stop being arrogant). So how insignificant is our knowledge anyway? I believe that it is so insignificant that there will always be something new to discover until the end of time.

May we all be given the heart to stay down to earth no matter how much we know...

Thinking about the choices we make

Whether we realize it or not, we are faced with options everyday.

We choose whether to take the bus or the train, to wake up early or late, to eat in or eat out, etc. The examples above are relatively easy to choices to make.

However, there are also times when we are faced with difficult ones, choices that will alter our way of life, such as when we are faced to choose a career, choose a partner in life (husband or wife), choose to have children or not, choose to do good or bad, choose a religion, etc. Even though we have made extensive research, there is still a large possibility that we become unsatisfied with the choices we make, and think that we've taken the wrong options.

So how do we know that we've made the right choices or not? Well, at the time we take the choice, we don't know for sure. All we can do is have confidence (hey, we've done our research right?), take the consequences and what is equally important, is to pray that our choices are correct and that whatever happens is for the best.

The maze of choices in life

Our life is like a maze with many right paths. Each choice we make contributes towards where we end up. But we have to beware that there are also dead ends. So pay attention to the clues and signs that might randomly show up. As in a maze, we can sometimes get lost in this world with all its offerings and glitters, which we should be aware of. For Muslims, we are lucky to be obliged to pray and be reminded for at least 17 times every day in our prayers to stay in the right path, "shiraathal ladziina an'amta 'alaihim", at least to protect our awareness.

May we all be guided on the path of righteousness, and be blessed with whatever choices we make in life.

Being grateful

I bet that everyone wants better things from what they have. Better earnings, better looks, better career, better computer, better car, better brain, better this, better that, better life...

Well let me tell you that it's perfectly human. One would always want better things from what one has. I guess we humans are cursed (and blessed) with this trait. It makes us progressive beings, who always seek for what is best.

Unfortunately, there are times when this trait makes us envious towards what other people have. And in turn make us ungrateful for what we ALREADY have. I know the feeling because I often experience it. If it gets too chronic and gets a hold on me, I become unfocused and spend a lot of energy on it (being envious and daydreaming takes quite an amount of energy you know...).

Anyway, the cure for envy is to be grateful for what we have. We often forget that the small details that God has given us are actually BIG blessings. The fact that we still have perfectly functional eyes to read this post is one of them. Having perfect hands to type with, having the luxury of internet connection, having the money to eat properly 3 times a day (sometimes more), being able to breath and all the little things that somehow slip our mind are all BIG blessings.

Being able to witness God's marvels are only one of the many blessings He has given us

Rather than looking up, try to look down to others that aren't as lucky as us. Say Alhamdulillahirabbil 'alamiin. "Praise be to Allah the lord of the worlds." And pledge ourselves to help those who are less lucky than us.

I hope we can all be grateful for the blessings that are given to us, and have tranquility in our hearts.

Our motives

Everything we do must have a reason, a motive behind it.

Our typical modern lives force our motivation to be dedicated to our family, career, money, hobby, lust, etc. And it is very difficult to create balance between them (for me anyway). There are also times where we get torn between our priorities, get obsessed into something and end up making a decision we regret. Furthermore, there might also be people who neglect common sense in order to pursue their ambition or motive, in the cost of other people.

In Islam, we are ordered to say Bismillahirahmaanirrahiim whenever we want to do anything. It is the opening verse of the Qur'an, which has meaning: "by the name of Allah, Most Gracious, Most Merciful". By saying this, we pledge ourselves in Allah's path, and all other motives blend and harmonize with it. We are ordered to do our best to become blessing for the universe, and to be beneficial for other people. It is supposed to create balance in our lives, and in turn make us better and happier people.

Nowadays, a lot of Muslims do not realize the philosophy behind "bismillahirahmaanirrahiim". They just say it as a formality, as a good luck charm, or just as a custom. This is far beyond what the sentence really means, and thus does not create the impact it is supposed to create.

I hope we are all given the wisdom and knowledge to grasp the best motivation to carry in our lives...

The purpose

As can be deduced from the title, this blog is dedicated to try to understand the Quran. I'm going to be using simple analogy and words for doing it. I believe that when we read the Quran (or any other books) with a clear heart and positive mind, we will find the beauty in what we read. Anyway, I am going to do my best to articulate what I can learn and find interesting. I believe there are many Muslims out there who don't fully understand what is written in the Quran (including myself), and others that are just curious about what is written in it.

Hopefully we can gain knowledge and better understanding on the Holy Quran, and share it with everyone else...

Systematic destruction through pirated software

I realize that this is going to be a long post, so whoever reads it, thanks for reading.

First of all, although I am against the use of pirated software, I am also not a big fan of those big companies who often overprice their products. Nevertheless, almost everyone knows that pirated software is against the law, but people still use it. I say “almost everyone” because some people really do not know the legal/illegal stance of pirated software (I was one of those people). But the fact that 80% of the software used around the world is pirated software is just simply overwhelming. It means that among 80% of PC users are (uhm, sorry) outlaws.

The amazing ease of getting access to pirated software is definitely one of the main reasons of its popularity. As if they were meant to be pirated. You can download a trial software, then do a google search to find the crack or key generator to the software, and then voila! You get the full version of it. You don’t need to dig into your wallet. All you need is an internet connection (and a computer of course). Yes, it is as easy as that. Trust me.

Microsoft products are among the most popular pirated software (I am not going to say victim because the term is relative). Most households in developing countries are almost certain to have a pirated version of windows and office. You would be amazed on how few people use LEGAL Microsoft software. Not justifying piracy in developing countries, but in my opinion, it seems rather harsh to price a product at $300 in a country which has a per capita income of $3500 like Indonesia (which means the average family has an income of $291 per month, although in reality it is much worse). So is Microsoft suffering any loss from this? In my opinion, it’s a big NO. Why? They get enough revenues from all their other big deals and rich people. Whether we realize it or not, nowadays, people depend so much on Microsoft’s software that it’s like marijuana to an addict.

One of the other popular piracy targets is Adobe’s photoshop. The software is highly rated among photographers and digital artists due to its versatility in manipulating and enhancing pictures and photos. Everyone wants to have it. Of course with Adobe’s near 1000 USD price tag they shouldn’t expect everyone to get a legal copy of the software. So is Adobe experiencing any loss here? Nope. Last that I heard their income has more than doubled over the past third quarter. Again, people become dependent on the software.

So there is a trend here. Letting everyone have software for free, in turn of addictedness. I don’t think it is such a big lost for the huge companies (in my opinion). But for users on the other hand, it is. For users like us, too good offers like pirated software are seldom turned down. We WANT (I repeat, want, not need) them so much, we’d do anything to get them, including “stealing” them. So, what do we become? As I said in a previous paragraph, outlaws. Whatever justification we make, we are still stealing from another person (even though we steal from gazillionaires like Microsoft’s Mr. Bill Gates). If we really NEED them as a career supporter, I am sure we will have the money to get legal copies, or at least plan to get one.

In all religions I know, stealing, whatever reason or from whomever we steal from is bad, a negative act. That negativity is invested to everything we do with those stolen items. We have to ask to ourselves, what goodness can we derive from stolen items?

By committing and supporting piracy, we have neglected universal justice and common sense. I hope we are all given the wisdom to look away from them, and use quality freeware, cheap alternatives, or buy the legal soft. I am sure nobody wants to be systematically converted into a thief.

I am truly sorry if anyone was offended by this post. I too am not able to be 100% consistent about this subject.

Nature’s Amazing Stability

Natural phenomena never stop to amaze me. A recent article in “Nature” reports that penguins changed their diet to krill in response to the steep decline in the whale and seal populations. The latter are krill predators, and the decline of their populations results in krill population “booming”. In order to keep the krill population stable, the penguins “made” krill their diet. Amazing!!

A happy (?) penguin family

Nature itself was designed to have high stability. The penguin–whale–krill relationship is just one of many examples of the stability mechanism in nature. The water cycle, plant photosynthesis, and even the work of our body (e.g. homeostasis) are all examples of stability mechanisms in nature. The complexity between components in nature (which still hold many unraveled mysteries) creates an amazingly sustainable system. Although we humans have done hundreds of years of research, we haven’t even touched the tip of fully understanding nature. There seems to always be something “new”, which shows us how “unknowledgeable” we really are.

Even law-protected forests are chopped down (Tanjung puting national park, picture courtesy of Greenpeace)

However, despite being highly durable, nature still faces serious contest with one of its own dominant components, humans. They drill the earth to look for buried goods, cut down trees (who have sustained us almost forever) to create toothpicks, blow out emission and gas from their BMWs, and do everything else you can think of to disturb natures stability. The penguin–whale–krill saga is also the result of human hands, with their whaling and sealing (which resulted in the decline of the whale/seal population). The saga has not yet ended though. Now, extensive krill exploitation is also predicted to have an impact on the penguin population.

Humans, the only real cause of nature's instability?

If we keep our attitude (to destroy things), what might be in store for us in the future? Disaster after disaster has begun, starting from mere landslides to the ultimate potential catastrophe of global warming. Nature itself, will always find a way to survive and reincarnate. However, components in it are dynamic and will always change. As demonstrated in species extinction (dinosaurs are one of the most famous).

Anyway, the next time nature faces an extreme condition that tests its stability, I wonder how it will comply. If a species is to be extinct, I wonder what will go? A plant species, an animal species, or …. us?

The Art of FREE Molecular Docking (Using DOCK 6.1) (Part 2)

Step by step docking

In this article, I am only going to SUPPLEMENT the tutorial provided at the DOCK website. Mainly the things which I found troublesome for me. So you should check out the tutorial first for a better understanding on the steps.

The steps in docking using DOCK are:

1) Structure preparation (enzyme and substrate)
For structure preparation, we will have to modify the 3D protein pdb file we have. I used a modeling program called Chimera (as what the tutorial advised), which is available free of charge from the Chimera website (http://www.cgl.ucsf.edu/chimera/). Structure preparation was a straight forward process. I mean, you only have to follow the tutorial to do so (it's already quite clear).

Just remember to prepare the charged mol2 structure of the ligand bound to the pdb protein's active site. You will need it if you want to be more efficient in the grid and sphere generating process. Even though you are not going to dock the ligand. I didn't identify this from the beginning, which created a problem in the sphgen - sphere generating procedure (it took too long, it could take for about 8 hours on my 1.6 Ghz centrino laptop with 512 RAM).

I did the structure preparations on windows, since I wasn't successful in installing the Chimera program on openSuse 10.2. Still remains a mystery for me up to now.

When you're finished with the preparation, now we can continue to the next step.

2) Sphere generation and selection
For generating the molecular surface of the protein, you will need a program called dms (as I have mentioned in my previous post). Installation was quite simple. Just type “make install” in the dms directory and stop there. You should have dms installed on your system (that's what happened to me in openSuse anyway). Remember that this is installation for a local machine. For parallel machines, there are other things you need to modify (check the dms readme that comes with the package).

When finished generating the molecular surface, use the program sphgen to generate the spheres.

Tip 1: copy the programs you want to use in your working directory!!.
Tip 2: in openSuse, instead of just typing “sphgen (options)”, I had to type “./sphgen (options)” to get it done!

After finished generating the spheres, now it's time to select the spheres you want to use as the active site. You can use the largest cluster created by sphgen, use a sphere in a selected radius, or select the spheres manually. I would recommend the second choice (use a sphere in a selected radius). Here, you should use the mol2 structure of the ligand bound to the pdb protein's active site (mentioned in step 1). This will save you precious time, believe me!

3) Grid generation
For this part, I had no problems at all. I just followed the tutorial, and I was home free.

4)Docking
There are 2 main ways of docking. First is the flexible ligand docking, and second is the rigid ligand docking. The flexible docking lets dock change the ligand conformation in response to the binding site. The rigid ligand doesn't let dock change ligand conformation. You should choose the one which suits your need.

For the docking process, thankfully I had no problems (I used flexible ligand docking). However, you might want to check the parameters that you need to tamper. For docking, I followed the dock v5.2.0 tutorial which is also available at the DOCK website.

Interpreting results
There are two main results that I found interesting (well, up to now, these are the only things I can analyze =)). First is the interaction energy of the ligand-protein complex. The lower the interaction energy, the stronger the bond is. I found this as additional data to supplement my kinetic experiments. Second is the conformation and orientation of the substrates in the binding site. Comparison with established ligand-protein structures can give better understanding on the effect of binding site structure has on substrate binding.

Well, this is a little taste of what DOCK can do for you. I have still much to learn about docking. But, since I am quite sure that it will be very important in future enzymatic studies, I have to spend more time to study it.

The Art of FREE Molecular Docking (Using DOCK 6.1) (Part 1)

Introduction and Installation

Enzymes play an important role in living organisms. They catalyze chemical reactions, where a substrate is converted into a product. Substrates are molecules that bind into the enzyme's active site where it undergoes conversion into the enzymatic product. I am not going to go too deep regarding enzymes, since you can find similar resources for this in the Internet (Wikipedia is a good place to start off).

What I am going to talk about, is a pragmatic way to better understand the interaction between an enzyme and its substrate using molecular modeling, in this case, docking using DOCK 6.1 (check the DOCK website at: http://dock.compbio.ucsf.edu). Well, mostly, I will be talking about my experience using the program, from installation to the docking process.

So what is docking?
Substrates, as do all molecules, have many different conformations they can take. The conformations play a determining factor in the way it binds to the active site of an enzyme. What also needs to be elucidated is the binding orientation, interaction energy (Ei), etc. One way to predict the orientation, conformation, and interaction energy (Ei) of an enzyme-substrate complex, is by molecular docking using in silico (computer) analysis. In short words, docking is meant to see the interaction between molecules and ligands (enzyme or protein). In my case, the data retrieved will then be analyzed to see substrate preference of the enzyme tested.

There is a wide range of programs that can be used for molecular docking, from freeware to expensive commercial wares. Among all, GOLD and Glide are considered to have the best accuracy. But to obtain one of them, you will need to invest at least around 3.200 USD. Too expensive for a student like me, and my lab hasn't allocated that much money to buy softwares. Anyway, for the solution, I tried to search for freewares. To my surprise, I found a lot of docking freewares. Among them are ArgusLab 4.0, Autodock, and DOCK.

At first, I tried ArgusLab 4.0, which was fairly easy to use. Installation was easy (it runs on windows XP), it has a nice GUI, and accompanied with an easy step by step tutorial, I was able to complete the docking process in no time (you can check out their website: http://www.planaria-software.com). However, the software isn't yet recognized in the scientific community. A quick search using the key word “Arguslab” in google scholar only resulted in 66 hits. There is even a comparison of Arguslab with GOLD, which shows that there are many things that needs to be improved in the current Arguslab version. Thus, I moved on to the other options.

Autodock was indeed tempting, however, the procedures to obtain a copy was somewhat “difficult”. You will need to send a fax or mail with the head of your institutes' signature on the license agreement. I am studying in Japan, and it takes time to complete procedures like that. That's why I moved on to DOCK 6.1. It wasn't hard to obtain, since you only have to fill in an on line request (with permission of your supervising Professor) to get it. I got the software after 2-3 days of my request. Lighting quick response.

So, I got the software, now what? Install it right? Well, it turned out not as easy as I suspected. To install DOCK, you will need a UNIX like environment. On windows, you can use a program called CYGWIN, which generates a UNIX like environment in windows. However, I opted to install openSuse linux (which is UNIX based) on my computer (I had a double OS booting). I compared the docking performance on both (cygwin and linux), and found that it was much more stable using the later (linux). The installation itself was sort of a trial and error process. You will need to install the compilers and other programs that are required to use DOCK (check the tab “dock related links” on their website). For a tutorial on installation of DOCK, you can see the DOCK manual (you will need to improvise though). I will make my own step by step installation soon.

Finished installing, you will have all the programs that you need in the /bin/ directory of your installation directory. However, you will need another program called “dms” (to compute molecular surface), which is not included in the DOCK package (you can get dms from: ftp://ftp.cgl.ucsf.edu/pub/dms.zip). I'll give details on installing it later.

There are 4 steps in docking with DOCK, which I will mention in my next post.

Who Took the Third Loaf of Bread?

I just heard this story from Yusuf Estes's site (www.shareislam.com), and find it interesting. The story was about Isa (Jesus) (Peace be upon him) and his companions during a journey. I hope we can all benefit from the moral and logic of the story.

Isa along with his companions were on a journey. During their journey, Isa, gave one of his apostles money and ordered him to buy some bread for their meal. The apostle did what Isa had ordered him to do and bought 3 loaves of bread for them to eat. However, the apostle was somehow afraid of not getting enough to eat, so he took the third loaf of bread and ate it for himself.

The apostle went back to Isa and gave him the 2 loaves of bread remaining. Isa, even though not knowing how many loaves of bread were bought, asked the apostle, “Where is the third loaf of bread?” The apostle replied, “There is no third loaf. The money was only enough to buy two.” Isa didn't reply, and all of them ate the two loaves of bread together.

In the middle of their journey, Isa and his companions hunted a deer. They killed the deer and they cooked it. While they were eating, Isa asked Allah to revive the deer. Just like that, the deer was revived and it jumped and ran away from them. And then Isa asked the apostle (who lied) again, “By the name of The One Who revived the deer, where is the third loaf of bread?” The apostle stood firm and replied, “There is no other loaf of bread, there were only two.” Again, Isa did not reply and they continued the journey.

Soon afterwards, they came to a flowing river. Isa asked his companions to hold his hands. Together, they walked on the water surface and crossed the river! Everyone was bemused. And once again, Isa asked the same apostle, “By the name of The One Who supplied this miracle, where is the third loaf of bread?” The apostle gave the same answer, “There was no third loaf of bread.” And again, Isa didn't reply and they continued their journey.

This time, they reached a dessert. Isa gathered 3 rocks, and asked Allah to turn them into gold. Isa gathered two huge chunks of gold and said, “We will divide this among us, and the one who took the last loaf of bread may have the third all to himself.” Voluntarily, the apostle who lied all along said, “It was I who took the third loaf of bread, so it is my right to have the last chunk of gold.” Isa then replied, “You can take all three, but you are no longer welcomed in this party.” The apostle (now ex-apostle) was so happy to receive the gold, that he didn't care about what Isa told him. He didn't even realize when Isa and the companions left.

While the ex-apostle was admiring the gold and dreaming about his future plans with it, three robbers spotted him. They stole the gold, and in the process, they also killed the ex-apostle. Afterwards, one of the robbers asked the other to buy some bread for them to eat. So off he went to buy bread (no, he didn't eat the bread). But greed whispered into his heart and he plotted to take all the gold for himself. How? He poisoned the bread that he bought. But little did he know, the other two robbers also plotted to take the gold for themselves, and planned to kill him. When the one who bought the bread came, the other two jumped him and killed him. In their joy, the two remaining robbers ate the bread (which was poisoned by the way) brought by the one they killed. And soon after, they died as well.

Soon after, Isa and his companions passed that spot and saw the dead ex-apostle, the three dead robbers, and the three chunks of gold. Isa as. then said, “This is what happens if you seek for worldly goods in life.” The gold was useless, and rather than doing good, it brought the death of the people who desired it.

Is bread worth "killing" honesty?

Is God still divine for us in life? In the world we know today, riches, money, a full tummy and other worldly goods are so tempting and virtually irresistible. We see many people sacrifice everything to get them. When we do get them, we always ask for more and more. Satisfaction is hard to achieve. And worst problem is that they become much more important than honesty, nobility, others lives, and even God Himself. I hope we are all among the ones who receive guidance, and be able to see the truth...

The Dajjal Inside of Us

Dajjal is a well-known character in the Islamic religion, which betrays the truth and sucks people in towards his defiance. Whether he is a real person or a system remains debatable. Christians may also know him as the “anti-christ”. He is said to be one of the signs of “the last day”.

The most dangerous of his characteristics is his ability to mislead people to think that good is bad; heaven is hell, and vice versa (he is also known as “the great deceiver”). However, if we open our hearts and be truthful, we will be able to identify Dajjal’s traps and stay away from them.

The 1 dollar one-eyed pyramid. The symbol of Dajjal??

The modern way of life demands us to reach for a successful career, power, plenty of riches, fun all the way, and other worldly pleasures, a one-dimensional view, which is an analogy of Dajjal’s one eye. Although at times we realize that we are lost and need a more proper goal in life, the pressure that is created around us by Dajjal’s system, forces us to go back to our “ordinary” lifestyle. As we get sucked in his defiance, we get more and more comfortable with the ride and tend to just play along. This way, our happiness will be illusive and short lasting.

Somehow, we have let him taken control of us. His clutches are so powerful that we have let little Dajjals grow inside of us now. His lust, his ambition and his spirit to create a world of ignorance, competition, pragmatism, and materialism have become what we breathe for. We live day by day to continue our routines without any real meaning in what we do. We do our best to improve our way of living, our comfort, yet we tend to forget/ignore what is happening around us.

How can we bear following tomorrow’s fashion trend, while there are still people that don’t even wear clothing? How can we still enjoy juicy thick beefsteaks while there are people that are dying because of hunger?

Still fancy yourself a luxurious dinner? Think again...

Is there no hope left? After these little Dajjals grow inside of us, is there any way to get rid of them?

Let us try to listen to our hearts more intensively. Seek what real happiness is, and let us break free from Dajjals clutches...

The Forgotten Republic of Indonecia

Even though my word processor gave a red underline for the title I wrote, suggesting that it is a spelling error, I can assure you it isn’t.

I took this photograph below when I picked up my wife at Kansai International Airport (Japan) in 2006 (I don’t know whether they have changed it or not). I don’t think that there is an airline called Garuda Indonecia. So, the sign must have meant Garuda Indonesia, but was miss spelled. A funny thing to encounter in an international class airport, and you don’t expect the Japanese to make many mistakes.

Fly with Garuda Indonecia?

The miss spell is kind of ironic, because the Indonesian – Japanese history is quite tied up to each other. Especially if we go back to 62–65 years ago (1942-1945), when the two countries were very “intimately” connected. The sad fact is that, even though most Indonesians are well aware of what happened then, not all Japanese are (maybe because they don’t teach “negative” history subjects in schools).

Is Indonesia that easy to forget?? :P

Global warming and thinking green

Global warming is no longer a POSSIBLE phenomenon. Global warming is already here, it's real and it’s happening at the point of “no return”. Global warming is happening presumably due to the accumulation of CO2 and other green house gases in the atmosphere. An article in Independent online published in February 2006, said that the global amount of CO2 in the atmosphere is already above its threshold, which is 400 ppm. Shockingly, the predicted amount (the time the article was published) was already 425 ppm. Whether we like it or not, we are now facing a time where the unpredictable will most likely happen.

The earth is changing...

In the past year, slight climate anomalies have happened all across the globe. Heat waves, hurricanes, melting ice caps, endless rain, and warm winters (no snow!! Can you believe that?), are all just glimpses of what might come to happen next. By 2100, the global temperature is predicted to rise up to 6oC with a 58-centimeter rise in sea level. In their recent report, the Intergovernmental Panel on Climate Change (IPCC) has charged MANKIND as the guilty party. So what's new? The question is, how did we do it, and what can we do now?

Plants are key organisms in maintaining our climate, because, along with several microbes, they are the only ones who can convert CO2 efficiently into Oxygen. Thus far, most of us have neglected the importance of plants in maintaining our way of life. From 1990 to 1997, every year we lost forests equal to 8285714 football (not American) fields. It means that every hour from 1990 to 1997, we lost forests equal to 945 football fields. The destruction nowadays might be even vaster. This amazing phenomenon itself is more than enough to cause the so-called global climate change (Not to mention the extensive CO2 released to the atmosphere by human activity, and other causes).

Our number one life supporter

Plants are invaluable to us. We have to be more aware of that. They are the only ones who can convert the sun’s energy to be able to be enjoyed by other beings, convert CO2 into oxygen that enables us to live, to breath and of course keeps CO2 from accumulating in the atmosphere (which is the main cause of global warming). From now on, it would definitely help if EVERYONE started thinking “green”. Protecting them means protecting us. Planting and growing them means investing for our future. And being aware of their condition means being aware of life itself. If all of us think "green", I’m sure we can make a difference.

Our Fortressed Education

For me, the ideal goal of “education” is to create minds that will build the community (or at least not burden it). When I say ideal, I truly hope that one day, it can be more than just a jargon. The prosperity and downfall of a community depends on the quality of its scholars. And the quality of a community’s scholars depends on the education they undergo. Wouldn’t it be nice if a community had bright scholars that are committed and focused on its development? But how can a scholar focus on building his community if he doesn’t know, doesn’t understand, and doesn’t feel connected to it?

The educational system in Indonesia (formal and informal) isolates the scholars from its community. It acts like a fortress that separates the so-called “intellectuals” and the so-called “people”. Once the “intellectuals” go back to the community, they are placed in places that are somewhat isolated from the “people”, where they gather with their same kind, thus forming a golden cage, which they enjoy by themselves. The “people” on the other hand, do not receive any benefit from the “intellectuals”, which they actually supported to flourish (indirectly).

Trapped by their state of mind, the “intellectuals” are then ignorant and have no significant role in the community’s development, which in turn makes the community stagnant (or even worse, degenerate), which might possibly be happening in Indonesia right now…

Let’s find the key to release our fear and ignorance, and let us regain our strength and courage to do what we think is right.

Nevertheless, I am pretty sure that many of Indonesia’s scholars have found that this mind cage does really exist, and are in the middle of finding the key to unlock it. I hope we can all contribute towards a better future for the people who need it (in any way possible).

Welcome My Son!!

Finally, after a fierce struggle of life and death, my wife gave birth to our beloved son. Welcome to this colorful yet challenging world“Saifan Seigi Ragamustari”!
I can’t say I have ever felt this happy, exited, and scared before.

We hope you grow up to be a good, kind, and strong person, and close to Allah nevertheless. And may Allah give my wife and me the power and strength to be good parents in every way.

He was born on the 14th of January 2007, 11.04 Japan time in Uji byouin (uji hospital), Uji, Kyoto, Japan. His birth weight was 2.922 kg, with a length of 48 cm.

Saifan and Mommy

Thank you Allah our dear lord. For giving us happiness and blessing through out our entire lives (Even though we tend to forget the good things and remember the bad things, lets stop doing that). Please pray for us my dear friends.

Once again, Welcome my son!!

The death of young potency

Being a youngster in a community isn’t always an advantage, especially in Indonesia. Sure, you get to be guided, taught, and somehow given less responsibility. But you sometimes do not get the respect and the acknowledgment you deserve. Older people tend to have delusions of grandeur that they are more experienced, smarter, stronger and wiser, and therefore deserve to have more respect than their younger counterparts. It seems like the younger you get, the less respect you get.

No respect means non-equal opportunities, and it is indeed a character killer. You are disregarded of your opinions, your ideas, your arguments, and abilities. Even though yours might be better.

Most Indonesians experience this at a very young age, where the older person is the teacher. Yes, at school. Teachers are never wrong. They are always right even though they are wrong. You aren’t supposed to draw a car jumping off a cliff, spiderman, a clown, etc. You are supposed to draw two mountain peaks, a road in the middle, and some paddy fields (the typical drawing of an indonesian youngster). You aren’t supposed to challenge your teacher’s ideas, if you don’t want to get bad grades. Don’t get me wrong. I respect my teachers. I am who I am partly because of them. But frankly, what teachers are doing nowadays is character killing, and what’s worse is that it’s contagious, and passed on to the next generation. It makes people blunt, dependent, scared (to express ideas) and uncreative. We need a way of teaching that “guides” yet not dominates.

This kind of “age superiority” is apparent in almost every aspect of an Indonesian’s life. In the politics, in the university, in business, and almost in everything else. The only thing that overcomes the dominancy of age, in most cases, is money (I guess).

By inhibiting growth and expansion of young, fresh, and not yet corrupted minds, the potency it has is slowly degraded. And the death of a nations young mind is death to the nation itself. This might explain why Indonesia is so fragile.

Let's become their guide and their inspiration

Nevertheless, what good can we do rather than by starting with ourselves. May we be among the people who respect their young, yet become their guide and their inspiration. (Gee, how will I be when I get old? Like I’m not old already :D)