Sequences encoding different information in DNA
Different information types corresponding with various DNA sequences exist in the genome. These DNA sequences that were considered junk for a long time because they were not coding proteins, have in fact been found to be responsible for an amazing array of functions in genomic structure. Some of these sequences include:
Group determining sequences that enable coordinated or successive expression of genes,
Sequences acting as a marker in charge of initiation and termination during transcription of DNA to RNA ,
Signal sequences responsible for conversion of primary immature RNA, sequences into smaller functional RNA molecules,
Transcription control sequences that determine the expression frequency of genes,
Sequences that identify and mark the initiation regions for intensification and remodeling of chromatins,
Sequences that make binding regions which affect the relocation of genome in nucleus or nucleolus,
Sequences that target regions where covalent DNA modification (methylation) with functional groups like methyl takes place,
Sequences that control and identify the regions responsible for initiation of DNA replication,
Sequences that make the structures which enable completion of replication at terminal ends,
Sequences at the segregation points that enable equal distribution of copied DNA molecules into daughter cells and centromere sequences,
Sequences responsible for guidance during repair of DNA bound errors and damages,
Start point sequences used for repackaging of genomes,
Recurring sequences exist in the genomes of many organisms and shows great structural diversity. Recurring elements function as an initiator or terminator for heterochromatin regions. Furthermore they form an important scaffold and binding spots for folding of DNA structure. As if they carry out the job of an architectural mold in specific shaping of genome to be packed into a very limited area. The ratio of repeating sequences in genome (60-90%) is much more than sequences that are encoding proteins and RNA (10-40%). To explain it with an example, chromosomes in human genome are made up of packages of protein-DNA such as heterochromatin and euchromatin. Heterochromatin regions usually make up the regions with no transcription whereas euchromatin regions feature DNA transcription.
The ratio of protein encoding sequences to the entire human DNA is approximately 1.2%. Around 43% of euchromatin regions are composed of recurring and mobile DNA elements. 18% of heterochromatin region is also made of satellite (dense repeating sequences) and mobile DNA elements. Therefore almost 50% of human genomic DNA is composed of these repeating DNA sequences. In bacteria however, these only make up around 5-10% of the genome. These sequences were described as parasitic and junk individual DNA structures up until today and still continues to be described thus by many researchers and scientist. Nevertheless, even today, mobile DNA elements and repeating sequences are accepted as genomic parasites. Recent advances in the last ten years that have demonstrated this is not true, have instead revealed the vital importance of repeating sequences in genomic functions.
Repeating DNA sequences affect chromatin (dense pack of DNA and protein) structure in two ways. Irregular repeating DNA sequence copies contain binding regions for proteins that organize DNA. Heterochromatin (darker since it is densely packed chromatin) inhibits transcription and recombination, delays replication, and generally blocks the reading of information in DNA sequences that contain genetic coding. Heterochromatin regions are distributed throughout the chromosome. Because of this, presence of regions with coupled successive repeated sequences triggers heterochromatin formation.
In fruit flies, placement of protein encoding loci required for eye pigmentation near the heterochromatin blocks in centromeres (phenomenon of position effect) is provided via organization of chromosomes and thus, formation of phenotypic characters are inhibited. The “phenomenon of position effect” is convincing evidence that genome is a major system which is integrated with composition of partially repeating DNA sequences. When heterochromatin amount is increased in XYY male fruit flies, reorganized pigmentation of eye expression decreases. In XO males, when heterochromatin amount decreases, inhibition becomes severe. Changes in levels of protein which binds to special heterochromatin specific DNA regions generate opposite effects. Decrease in these proteins reduces or suppresses “phenomenon of position effect.” Surplus synthesis of these proteins also enriches this effect.
Repeating DNA sequences play an important role in the transfer of genome into daughter cells. For instance, they function in formation of the centromeres as chromosomal binding regions for microtubules, during gamete formation as linear terminals of chromosomes are replicated, and during chromosomal matching. Distribution of repeating sequences plays a major role in configuration of genomic functions. Each genome has genomic system structure that is shaped dependent on the amount of repeating DNA sequences to a major extent.
Going back to Nursi’s explanation of the Manifest Record, we can draw a parallelism between the book of the universe and the book of revelation, the first of which shows us that certain sequences in the genome are repeated for significance and necessity, just as many verses are repeated frequently in the Qur’an with nuances to refer to different meanings, benefits, and purposes, opening a wider space for many interpretations.
A genome is not only a book that contains protein and RNA codes, but also has a complex system structure with many functions for cellular vitality. The most needed sequences are those that are repeated more frequently. They are not pieces of junk DNA as predicted, they are jewels Divinely constructed.
Muhammad Shah was the last prince but one of the Khwarazm dynasty of Balkh, to which family both the poet’s mother and grandmother belonged. He was the reigning prince in AD. 1209, the year in which the poet’s father fled from Balkh, and was defeated by Chingiz Khan a year or two later. In one of his campaigns Muhammad Shah captured the city of Sabzawar, in Khorasan, which city as inhabited by Rafizis or rank Shi'as, naturally most obnoxious to a Sunni prince claiming descent from the first Khahif Abu Bakr. After the city was taken the inhabitants came out, and proceeded with all humility to beg their lives, offering to pay any amount of ransom and tribute that he might impose upon them. But the prince replied that he would spare their lives only on one condition, viz., that they produced from Sabzawar a man bearing the name Abu Bakr. They represented to him that it would be impossible to find in the whole city a single man bearing a name so hateful to the Shi'as; but the prince was inexorable, and refused to alter the conditions. So they went and searched all the neighbourhood, and at last found a traveler lying at the roadside at the point of death, who bore the name of Abu Bakr. As he was unable to walk, they placed him on a bier and carried him into the king’s presence. The king reproached them for their contempt and neglect of this pious Sunni, the only true heart amongst them, and reminded them of the saying of the Prophet, “God regards not your outward show and your wealth, but your hearts and your deeds.” In this parable, says the poet, Sabzawar is the world, the poor Sunni the man of God, despised and rejected of men, and the king is God Almighty, who seeks a true heart amongst evil men.
Satan’s snares for mankind.
Thus spake cursed Iblis to the Almighty,
“I want a mighty trap to catch human game withal.”
God gave him gold and silver and troops of horses
Saying, “You can catch my creatures with these.”
Iblis said, “Bravo!” but at the same time hung his lip,
And frowned sourly like a bitter orange.
Then God offered gold and jewels from precious mines
To that laggard in the faith,
Saying, “Take these other traps, O cursed one.”
But Iblis said, “Give me more, O blessed Defender.”
God gave him succulent and sweet and costly wines,
And also store of silken garments.
But Iblis said, “ O Lord, I want more aids than these,
In order to bind men in my twisted rope
So firmly that Thy adorers, who are valiant men
May not, man-like, break my bonds asunder.”
When at last God showed him the beauty of women,
Which bereaves men of reason and self-control,
Then Iblis clapped his hands and began to dance,
Saying, “Give me these; I shall quickly prevail with these!”
This is followed by comments on the text, “Of goodliest fabric we created man, and then brought him down to the lowest of the low, saving those who believe and do the things that are right;” 1 and on the verses,
“If thou goest the road, they will show thee the road;
If thou becomest naught, they will turn thee to being.”
1. Koran xcv. 4.
Kalau kita menginginkan sebuah kesuksesan. Maka, izinkan diri untuk berproses
Every situation has two handles.
Which one will you drive?
Will you choose the road paved with an appreciation for precious lessons or will you drive down the spiral of anger and resentment?
Which attitude can take you to a higher, more rewarding destination?
In the Name of Allah, the Most Gracious, the Most Merciful
4. Indeed there has been an excellent example for you in Ibrahim and those with him, when they said to their people:
“Verily, we are free from you and whatever you worship besides Allah, we have rejected you, and there has started between us and you, hostility and hatred forever until you believe in Allah alone,” – except the saying of Ibrahim to his father:
“Verily, I will ask forgiveness for you, but I have no power to do anything for you before Allah.”
“Our Lord! In You we put our trust, and to You we turn in repentance, and to You is the final Return.”
5. “Our Lord! Make us not a trial for the disbelievers, and forgive us, Our Lord! Verily, You, only You, are the Almighty, the All-Wise.”
6. Certainly, there has been in them an excellent example for you to follow - for those who look forward to (the meeting with) Allah and the Last Day.
And whosoever turns away, then verily, Allah is Al- Ghani, Al-Hamid.
The Good Example of Ibrahim and His Followers, when They disowned Their Disbelieving People
Allah the Exalted says to His faithful servants, whom He commanded to disown the disbelievers, to be enemies with them, and to distant themselves and separate from them:
Indeed there has been an excellent example for you in Ibrahim and those with him, meaning, his followers who believed in him, when they said to their people: “Verily we are free from you…” meaning, `we disown you,’ and whatever you worship besides Allah: we rejected you, meaning, `we disbelieve in your religion and way,’ and there has started between us and you, hostility and hatred forever.
meaning, `Animosity and enmity have appeared between us and you from now and as long as you remain on your disbelief; we will always disown you and hate you,’ meaning, `unless, and until, you worship Allah alone without partners and disbelieve in the idols and rivals that you worship besides Him.’
Allah’s statement, except the saying of Ibrahim to his father: “Verily, I will ask forgiveness (from Allah) for you…”, means, `you have a good example in Ibrahim and his people; as for Ibrahim’s prayers to Allah for his father, it was a promise that he made for his father.’ When Ibrahim became sure that his father was an enemy of Allah, he declared himself innocent of him.
Some of the believers used to invoke Allah for their parents who died as disbelievers, begging Him to forgive them. They did so claiming that Ibrahim used to invoke Allah to forgive his father.
Allah the Exalted said in reply,
It is not for the Prophet and those who believe to ask Allah’s forgiveness for the idolators, even though they be of kin, after it has become clear to them that they are the dwellers of the Fire (because they died in a state of disbelief). And Ibrahim’s request for his father’s forgiveness was only because of a promise he made to him. But when it became clear to him that he was an enemy of Allah, he dissociated himself from him. Verily, Ibrahim was Awwah and was forbearing. (9:113-114)
Allah said here,
Indeed there has been an excellent example for you in Ibrahim and those with him, when they said to their people: “Verily, we are free from you…” until, … except the saying of Ibrahim to his father: “Verily, I will ask forgiveness for you, but I have no power to do anything for you before Allah.”
meaning, `You cannot follow Ibrahim’s example as proof in the case mentioned here, as being allowed to ask Allah to forgive those who died on Shirk.’
This is the saying of Ibn Abbas, Mujahid, Qatadah, Muqatil bin Hayyan, Ad-Dahhak and several others. Allah the Exalted said that Ibrahim and his companions, who parted with their people and disowned their way, said afterwards, while invoking Allah in humility and submission,
Our Lord! In You we put our trust, and to You we turn in repentance, and to You is the final Return.
meaning, `we trust in You for all matters, we surrender all of our affairs to You, and to You is the final Return in the Hereafter,’
Our Lord! Make us not a trial for the disbelievers, Mujahid said,
“It means, `Do not punish us by their hands, nor with a punishment from You.’ Or they will say, `Had these people been following the truth, the torment would not have struck them’.”
Ad-Dahhak said something similar. Qatadah said,
“Do not give the disbelievers victory over us, thus subjecting us to trials by their hands. Surely, if You do so, they would then think that they were given victory over us because they are on the truth.”
This is the meaning that Ibn Jarir preferred.
Ali bin Abi Talhah reported from Ibn `Abbas:
“Do not give them dominance over us, lest we suffer trials by their hands.“
Allah’s statement, and forgive us, Our Lord! Verily, You, only You, are the Almighty, the All-Wise.
means, `cover our mistakes from being exposed to other than You, and forgive us for what (sin) is between us and You.’
(Verily, You, only You, are the Almighty), `and those who seek refuge in Your majesty are never dealt with unjustly, (the All-Wise), `in Your statements, actions, legislation and decrees.’
Allah the Exalted said,
Certainly, there has been in them an excellent example for you to follow – for those who look forward to (the meeting with) Allah and the Last Day, asserting what He has said before with the exemption mentioned, i.e., the good example that Allah mentioned before, (for those who look forward to Allah and the Last Day), thus encouraging the believers who believe in Allah and the Return to Him.
And whosoever turns away, meaning, from what Allah has ordained, verily, Allah is Al-Ghani, Al-Hamid.
Allah said in another Ayah,
If you disbelieve, you and all on the earth together, then verily! Allah is Ghani, Hamid. (14:8)
Ali bin Talhah reported from Ibn `Abbas, Ghani, is the One Who is perfectly rich.”
That is Allah. This is Allah’s attribute that He alone is worthy of being described by; surely, He has no equal, none like unto Him. All praise is due to Allah, the One, the Irresistible.
Hamid means, the praiseworthy, in all His statements and actions, there is no (true) God except Him alone.
💐 In The Name Of Allah The Most Gracious The Most Merciful
💌 Wherever we go on earth, so long as we’re alive,
We’re given problems to solve every once in a while -
From monetary problems to tests in marriage life,
Social dilemmas, crisis where the strong ones survive,
And tough choices to make, to follow one’s heart or mind.
“Can I reach out to them? Will they listen or backbite?”
“Should I strengthen this connection? Is this bond worthwhile?”
“Yes I’ve forgiven them, but I’m still hurting inside.”
And “Who is worth trusting when all humans can tell lies?”
Are some of my worries that visit once in a while.
“The income I receive, is it halal or defiled?”
“The news I often read, which of it conceals a lie?”
“Souls destined for me to meet, on them can I rely?”
Distractions, temptations and other evil desires
Are from life’s problems that can be difficult to fight.
Then again, “Allah is with us,” ourselves let’s remind.
We can talk to Allah anytime, when sad or tired,
When most of humanity would abandon our side.
Solutions to problems: Saying Du'a day and night,
Trusting Allah, Sabr, and awaiting Paradise.
📖 Abu Sa’eed Al-Khudri RadhiAllahu ‘anhu narrated: Allah’s noble Messenger Muhammad SallAllahu 'alaihi wa sallam said, “There is no Muslim who calls upon Allah, without sin or cutting family ties, but that Allah will give him one of three answers: He (Allah Subhaanahu wa Ta'aala) will quickly fulfill his supplication, He will store it for him in the Hereafter, or He will divert an evil from him similar to it.” They said, “In that case we will ask for more.” The Prophet SallAllahu 'alaihi wa sallam said, “Allah has even more.”
Source: Musnad Aḥmed 10749
Grade: Sahih (Authentic) according to Al-Albani
📖 Abu Huraira RadhiAllahu 'anhu narrated: Allah’s noble Messenger Muhammad SallAllahu 'alaihi wa sallam said, “Our Rabb (Allah Subhaanahu wa Ta'aala) descends to the lowest heaven in the last third of every night, and He says: 'Who is calling upon Me so that I may answer him? Who is asking from Me so that I may give him? Who is seeking My Forgiveness so that I may forgive him?’”
Source: Sahih Al-Bukhari 1094
Sahih Muslim 758
Grade: Muttafaqun Alayhi (Authenticity agreed upon) according to Al-Bukhari and Muslim
📖 Abu Huraira RadhiAllahu 'anhu narrated: Allah’s noble Messenger Muhammad SallAllahu 'alaihi wa sallam said, “Call upon Allah with certainty that He will answer you. Know that Allah will not answer the supplication of a heart that is negligent and distracted.”
Source: Sunan At-Tirmidhī 3479
Grade: Hasan (Fair) according to Al-Albani
Morals are a set of noble principles that originate in high spirituality and govern human conduct. For this reason, people who neglect spirituality, and are therefore lacking in spiritual values, cannot sustain conduct in accordance with these principles. Preferring the interests of others over one’s own is high spirituality and liberality. Those who always do good without expecting any return one day will bow before God in wonder and admiration when, unexpectedly, they meet the accumulated results of their considerate nature and all the good they have done.
Just because you are a learned one does not mean that you are truly human. Learned people are freed from carrying the burden of superfluous information and attain greatness to the extent that they serve humanity and set a good example for others through their high morals and virtues. Otherwise, they are no more than people who have wasted their lives. Those with high morals and virtues, even if they lack learning and as dense as iron, may sometimes prove to be a useful and valuable, and even as good as gold. Never deceive anyone, even if they deceive you. Fidelity and uprightness are two of the highest virtues. Even if following this advice brings you loss, which it usually does, always be faithful and upright.
Morals were once thought of as virtues. Today, morals are regarded as a collection of rules for social behavior. I wish people would behave in accordance with those rules, even though they are not virtuous! In the past, people would say: “The principles of good conduct are no longer practiced; we only see them written down in books.” Today, they say: “The principles of good conduct are out of date; whatever remains of them is written down in old books.” Whatever they say, those principles are worth the sacrifice of many new things, even though people try to present them as outdated.
Bismillah Walhamdulillah Was Salaatu Was Salaam ‘ala Rasulillah Narrated Abu Huraira (Radi-Allahu 'anhu):
Allah’s Apostle (Sallallahu 'Alaihi Wa Sallam) said, “During your sleep, Satan knots three knots at the back of the head of each of you, and he breathes the following words at each knot, 'The night is, long, so keep on sleeping,’ If that person wakes up and celebrates the praises of Allah, then one knot is undone, and when he performs ablution the second knot is undone, and when he prays, all the knots are undone, and he gets up in the morning lively and gay, otherwise he gets up dull and gloomy.”
Bukhari Vol. 4 : No. 491
The Prophet said that “cleanliness is half of faith.” Therefore, we should recognize the importance of both inward and outward cleanliness, and keep our living quarters and environment clean.
In Islam there is a great emphasis on cleanliness, both physi- cal and spiritual. After the occasion of the first revelation of a verse of the Qur’an (“Read!”), the second verse to be revealed was a command about wearing clean clothing: “O you cloaked one (who has preferred solitude)! Arise and warn! And declare your Lord’s (inde- scribable and incomparable) greatness. And keep your clothing clean! Keep away from all pollution” (Muddaththir 74:1–5).
The Islamic scholar Elmalili Hamdi Yazir interprets the word siyab (usually “clothing”) in this verse to signify the “soul” and the “heart.” Thus, he paraphrases the verse as “keep yourself and your heart clean from sin and unrighteousness, stay away from unclean feelings that will ruin your good deeds, and clothe yourself in good morality so that your good works may be acceptable.” But Yazir al- so sees no problem with a literal understanding of the verse, direct- ly referring to physical and outward cleanliness, as well. Thus, it is highly likely that the verse is also a commandment to keep the body and its garments clean.71
It is clear that this responsibility—to keep oneself clean, both from outward impurities as well as from sins, like ascribing part- ners to God, rebellion against God, hypocrisy, and so on—is a moral obligation demanded by Islam. Both types of uncleanness are mentioned together in another Qur’anic verse: “Surely God loves
those who turn to Him in sincere repentance (of past sins and errors)
and He loves those who cleanse themselves” (Baqara 2:222).
The first requirement for deserving God’s love, entering His Presence, and being His servant is cleanliness. It is the first thing we must do to put ourselves in the correct state for performing obligatory daily prayers, which are the “ascension of the believer.” In the following verse God decrees performing ablution or taking a bath for this purpose:
O you who believe! When you rise up for the Prayer, (if you have no ablution) wash your faces and your hands up to (and including) the elbows, and lightly rub your heads (with water) and (wash) your feet up to (and including) the ankles. And if you are in the state of major ritual impurity (requiring total ablution), purify yourselves (by taking a bath)…. (Maeda 5:6)
With this verse the ablutions before ritual prayers became obligatory and all Muslims wash their hands, faces, mouths, noses, ears, necks, and feet before each of the five daily prayers.
Just as we should keep our body and the clothes we wear clean, we also need to keep our living quarters and the places where we worship clean. The Qur’an says, “O children of Adam! Dress cleanly
and beautifully for every act of worship…” (A’raf 7:31). God’s
Messenger made it an obligatory practice to bathe at least once a week (this was at a time when frequent bathing was uncommon).72 He also instructed people to “keep your environment clean”73 and urged them to maintain the shared community spaces as well. A ha- dith recounts his words on this subject: “Avoid two cursed things,” he said, and when the Companions asked “What two things?” he re- plied, “Relieving oneself on the road where people pass by, or in a shady place (where people take a rest).”74
Prophet Muhammad, who was “the Living Qur’an” and who embodied Qur’anic morality, as with everything, was the best of examples in cleanliness. He was very careful about his own cleanli- ness and whenever he lay down or got up, day or night, he washed his mouth and nose, brushed his teeth75 and made ablutions.76 In particular he emphasized that cleaning the teeth is crucial not only for the health of our mouth, but also to please God77; moreover, he taught that the first thing a person should do on waking from sleep is to wash their hands.78 He was also careful to dry his limbs on a towel after washing.79 God’s Messenger paid close attention to cleanliness throughout his life; he would wear clean, nice clothes whenever he out went in public, particularly to the mosque or to visit someone. He used pleasant scents and avoided eating onions, garlic or smelly foods before going out.