498)How Cells Work: The Miniscule, Ordered, Dynamic And Thriving Universe Inside A Cell; Quotes of Aga Khan IV and Others.

How Cells Work
by Marshall Brain

Browse the article How Cells Work


Introduction to How Cells Work

DNA PicturesThe human body is composed of about 10 trillion cells. Everything from reproduction to infections to repairing a broken bone happens down at the cellular level. Find out all about cells. See more DNA pictures.

­At a microscopic level, we are all composed of cells. Look at yourself in a mirror -- what you see is about 10 trillion cells divided into about 200 differen­t types. Our muscles are made of muscle cells, our livers of liver cells, and there are even very specialized types of cells that make the enamel for our teeth or the clear lenses in our eyes!

If you want to ­understand how your body works, you need to understand cells. Everything from reproduction to infections to repairing a broken bone happens down at the cellular level. If you want to understand new frontiers like biotechnology and genetic engineering, you need to understand cells as well.

Anyone who reads the paper or any of the scientific magazines (Scientific American, Discover, Popular Science) is aware that genes are BIG news these days. Here are some of the terms you commonly see:

Biotechnology
Gene splicing
Human genome
Genetic engineering
Recombinant DNA
Genetic diseases
Gene therapy
DNA mutations
DNA fingerprinting or DNA profiling

­Gene science and genetics are rapidly changing the face of medicine, agriculture and even the legal system!

In this article, we'll delve down to the molecular level to completely understand how cells work. We'll look at the simplest cells possible: bacteria cells. By understanding how bacteria work, you can understand the basic mechanisms of all of the cells in your body. This is a fascinating topic both because of its very personal nature and the fact that it makes these news stories so much clearer and easier to understand. Also, once you understand how cells work, you will be able to answer other related questions like these:

What is a virus and how does it work at the molecular level?
What is an antibiotic and how do antibiotics work? Why don't antibiotics kill normal cells?
What is a vitamin, and why do we need to take them every day?
How do poisons work?
What does it mean to be alive, at least at the cellular level? All of these questions have obvious answers once you understand how cells work -- so let's get started!

­
Cell Parts

Your body is made of about 10 trillion cells. The largest human cells are about the diameter of a human hair, but most human cells are smaller -- perhaps one-tenth of the diameter of a human hair.

Run your fingers through your hair now and look at a single strand. It is not very thick -- maybe 100 microns in diameter (a micron is a millionth of a meter, so 100 microns is a tenth of a millimeter). A typical human cell might be one-tenth of the diameter of your hair (10 microns). Look down at your little toe -- it might represent 2 or 3 billion cells or so, depending on how big you are. Imagine a whole house filled with baby peas. If the house is your little toe, the peas are the cells. That's a lot of cells!

Bacteria are about the simplest cells that exist today. A bacteria is a single, self-contained, living cell. An Escherichia coli bacteria (or E. coli bacteria) is typical -- it is about one-hundredth the size of a human cell (maybe a micron long and one-tenth of a micron wide), so it is invisible without a microscope. When you get an infection, the bacteria are swimming around your big cells like little rowboats next to a large ship.

Bacteria are a lot simpler than human cells. A bacterium consists of an outer wrapper called the cell membrane, and inside the membrane is a watery fluid called the cytoplasm. Cytoplasm might be 70-percent water. The other 30 percent is filled with proteins called enzymes that the cell has manufactured, along with smaller molecules like amino acids, glucose molecules and ATP. At the center of the cell is a ball of DNA (similar to a wadded-up ball of string). If you were to stretch out this DNA into a single long strand, it would be incredibly long compared to the bacteria -- about 1000 times longer!

See picture:
An E. coli bacterium has a distinctive, capsule shape. The outer portion of the cell is the cell membrane, shown here in orange. In E. coli, there are actually two closely-spaced membranes protecting the cell. Inside the membrane is the cytoplasm, made up of millions of enzymes, sugars, ATP and other molecules floating freely in water. At the center of the cell is its DNA. The DNA is like a wadded-up ball of string. There is no protection for the DNA in a bacterium -- the wadded-up ball floats in the cytoplasm roughly in the center of the cell. Attached to the outside of the cell are long strands called flagella, which propel the cell. Not all bacterium have flagella, and no human cells have them besides sperm cells.

Human cells are much more complex than bacteria. They contain a special nuclear membrane to protect the DNA, additional membranes and structures like mitochondria and Golgi bodies, and a variety of other advanced features. However, the fundamental processes are the same in bacteria and human cells, so we will start with bacteria.


Enzymes

At any given moment, all of the work being done inside any cell is being done by enzymes. If you understand enzymes, you understand cells. A bacterium like E. coli has about 1,000 different types of enzymes floating around in the cytoplasm at any given time.

Enzymes have extremely interesting properties that make them little chemical-reaction machines. The purpose of an enzyme in a cell is to allow the cell to carry out chemical reactions very quickly. These reactions allow the cell to build things or take things apart as needed. This is how a cell grows and reproduces. At the most basic level, a cell is really a little bag full of chemical reactions that are made possible by enzymes!

Enzymes are made from amino acids, and they are proteins. When an enzyme is formed, it is made by stringing together between 100 and 1,000 amino acids in a very specific and unique order. The chain of amino acids then folds into a unique shape. That shape allows the enzyme to carry out specific chemical reactions -- an enzyme acts as a very efficient catalyst for a specific chemical reaction. The enzyme speeds that reaction up tremendously.

For example, the sugar maltose is made from two glucose molecules bonded together. The enzyme maltase is shaped in such a way that it can break the bond and free the two glucose pieces. The only thing maltase can do is break maltose molecules, but it can do that very rapidly and efficiently. Other types of enzymes can put atoms and molecules together. Breaking molecules apart and putting molecules together is what enzymes do, and there is a specific enzyme for each chemical reaction needed to make the cell work properly.

See picture: The chemical structure of glucose
Photo courtesy -->Maltose is made of two glucose molecules bonded together (1). The maltase enzyme is a protein that is perfectly shaped to accept a maltose molecule and break the bond (2). The two glucose molecules are released (3). A single maltase enzyme can break in excess of 1,000 maltose bonds per second, and will only accept maltose molecules.

You can see in the diagram above the basic action of an enzyme. A maltose molecule floats near and is captured at a specific site on the maltase enzyme. The active site on the enzyme breaks the bond, and then the two glucose molecules float away.

You may have heard of people who are lactose intolerant, or you may suffer from this problem yourself. The problem arises because the sugar in milk -- lactose -- does not get broken into its glucose components. Therefore, it cannot be digested. The intestinal cells of lactose-intolerant people do not produce lactase, the enzyme needed to break down lactose. This problem shows how the lack of just one enzyme in the human body can lead to problems. A person who is lactose intolerant can swallow a drop of lactase prior to drinking milk and the problem is solved. Many enzyme deficiencies are not nearly so easy to fix.

Inside a bacterium there are about 1,000 types of enzymes (lactase being one of them). All of the enzymes float freely in the cytoplasm waiting for the chemical they recognize to float by. There are hundreds or millions of copies of each different type of enzyme, depending on how important a reaction is to a cell and how often the reaction is needed. These enzymes do everything from breaking glucose down for energy to building cell walls, constructing new enzymes and allowing the cell to reproduce. Enzymes do all of the work inside cells.


Proteins

A protein is any chain of amino acids. An amino acid is a small molecule that acts as the building block of any protein. If you ignore the fat, your body is about 20-percent protein by weight. It is about 60-percent water. Most of the rest of your body is composed of minerals (for example, calcium in your bones).

Amino acids are called "amino acids" because they contain an amino group (NH2) and a carboxyl group (COOH) that is acidic. In the figure above, you can see the chemical structure of two of the amino acids. You can see that the top part of each one is the same. That is true of all amino acids -- the little chain at the bottom (the H or the CH3 in these two amino acids) is the only thing varying from one amino acid to the next. In some amino acids, the variable part can be quite large. The human body is constructed of 20 different amino acids (there are perhaps 100 different amino acids available in nature).

As far as your body is concerned there are two different types of amino acids: essential and non-essential. Non-essential amino acids are amino acids that your body can create out of other chemicals found in your body. Essential amino acids cannot be created, and therefore the only way to get them is through food. Here are the different amino acids:


Non-essential:

Alanine (synthesized from pyruvic acid)
Arginine (synthesized from glutamic acid)
Asparagine (synthesized from aspartic acid)
Aspartic acid (synthesized from oxaloacetic acid)
Cysteine (synthesized from homocysteine, which comes from methionine)
Glutamic acid (synthesized from oxoglutaric acid)
Glutamine (synthesized from glutamic acid)
Glycine (synthesized from serine and threonine)
Proline (synthesized from glutamic acid)
Serine (synthesized from glucose)
Tryosine (synthesized from phenylalanine)


Essential:

Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

Protein in our diets comes from both animal and vegetable sources. Most animal sources (meat, milk, eggs) provide what's called "complete protein", meaning that they contain all of the essential amino acids. Vegetable sources usually are low on or missing certain essential amino acids. For example, rice is low in isoleucine and lysine. However, different vegetable sources are deficient in different amino acids, and so by combining different foods you can get all of the essential amino acids throughout the course of the day. Some vegetable sources contain quite a bit of protein. Nuts, beans and soybeans are all high in protein. By combining them, you can get complete coverage of all essential amino acids.

The digestive system breaks all proteins down into their amino acids so that they can enter the bloodstream. Cells then use the amino acids as building blocks to build enzymes and structural proteins.

See How Food Works for additional information.


Enzymes at Work

There are all sorts of enzymes at work inside of bacteria and human cells, and many of them are incredibly interesting! Cells use enzymes internally to grow, reproduce and create energy, and they often excrete enzymes outside their cell walls as well. For example, E. coli bacteria excrete enzymes to help break down food molecules so they can pass through the cell wall into the cell. Some of the enzymes you may have heard of include:

Proteases and peptidases - A protease is any enzyme that can break down a long protein into smaller chains called peptides (a peptide is simply a short amino acid chain). Peptidases break peptides down into individual amino acids. Proteases and peptidases are often found in laundry detergents -- they help remove things like blood stains from cloth by breaking down the proteins. Some proteases are extremely specialized, while others break down just about any chain of amino acids. (You may have heard of protease inhibitors used in drugs that fight the AIDS virus. The AIDS virus uses very specialized proteases during part of its reproductive cycle, and protease inhibitors try to block them to shut down the reproduction of the virus.)

Amylases - Amylases break down starch chains into smaller sugar molecules. Your saliva contains amylase and so does your small intestine. Maltase, lactase, sucrase (described in the previous section) finish breaking the simple sugars down into individual glucose molecules.

Lipases - Lipases break down fats.

Cellulases - Cellulases break cellulose molecules down into simpler sugars. Bacteria in the guts of cows and termites excrete cellulases, and this is how cows and termites are able to eat things like grass and wood.

Bacteria excrete these enzymes outside their cell walls. Molecules in the environment are broken down into pieces (proteins into amino acids, starches into simple sugars, etc.) so they are small enough to pass through the cell's wall into the cytoplasm. This is how an E. coli eats!


Inside a cell, hundreds of highly specialized enzymes carry out extremely specific tasks that the cell needs to live its life. Some of the more amazing enzymes found inside cells include:

Energy enzymes - A set of 10 enzymes allows a cell to perform glycolysis. Another eight enzymes control the citric-acid cycle (also known as the Krebs cycle). These two processes together allow a cell to turn glucose and oxygen into adenosine triphosphate, or ATP. In an oxygen-consuming cell like E. coli or a human cell, one glucose molecule forms 36 ATP molecules (in something like a yeast cell, which lives its life without oxygen, only glycosis occurs and it produces only two ATP molecules per glucose molecule). ATP is a fuel molecule that is able to power enzymes by performing "uphill" chemical reactions.

Restriction enzymes - Many bacteria are able to produce restriction enzymes, which recognize very specific patterns in DNA chains and break the DNA at those patterns. When a virus injects its DNA into a bacterium, the restriction enzyme recognizes the viral DNA and cuts it, effectively destroying the virus before it can reproduce.

DNA-manipulation enzymes - There are specialized enzymes that move along DNA strands and repair them. There are other enzymes that can untwist DNA strands to reproduce them (DNA polymerase). Still others can find small patterns on DNA and attach to them, blocking access to that section of DNA (DNA-binding proteins).

Enzyme-production enzymes - All of these enzymes have to come from somewhere, so there are enzymes that produce the cell's enzymes! Ribonucleic acid (RNA), in three different forms (messenger RNA, transfer RNA and ribosomal RNA), is a big part of the process. A cell really is nothing but a set of chemical reactions, and enzymes make those reactions happen properly.


Making Enzymes

As long as a cell's membrane is intact and it is making all of the enzymes it needs to function properly, the cell is alive. The enzymes it needs to function properly allow the cell to create energy from glucose, construct the pieces that make up its cell wall, reproduce and, of course, produce new enzymes.

So where do all of these enzymes come from? And how does the cell produce them when it needs them? If a cell is just a collection of enzymes causing chemical reactions that make the cell do what it does, then how can a set of chemical reactions create the enzymes it needs, and how can the cell reproduce? Where does the miracle of life come from?

The answer to these questions lies in the DNA, or deoxyribonucleic acid. You have certainly heard of DNA, chromosomes and genes. DNA guides the cell in its production of new enzymes.

The DNA in a cell is really just a pattern made up of four different parts, called nucleotides or bases. Imagine a set of blocks that has only four different shapes, or an alphabet that has only four different letters. DNA is a long string of blocks or letters. In an E. coli cell, the DNA pattern is about 4 million blocks long. If you were to stretch out this single stand of DNA, it would be 1.36 mm long -- pretty long considering the bacteria itself is 1,000 times smaller. In bacteria, the DNA strand is like a wadded-up ball of string. Imagine taking 1,000 feet (300 meters) of incredibly thin thread and wadding it up -- you could easily hold it in your hand. [A human's DNA is about 3 billion blocks long, or almost 1,000 times longer than an E. coli's. Human DNA is so long that the wadded-up approach does not work. Instead, human DNA is tightly wrapped into 23 structures called chromosomes to pack it more tightly and fit it inside a cell.]

The amazing thing about DNA is this: DNA is nothing more than a pattern that tells the cell how to make its proteins! That is all that DNA does. The 4 million bases in an E. coli cell's DNA tell the cell how to make the 1,000 or so enzymes that an E. coli cell needs to live its life. A gene is simply a section of DNA that acts as a template to form an enzyme.

Let's look at the entire process of how DNA is turned into an enzyme so you can understand how it works.


DNA

You have probably heard of the DNA molecule referred to as the "double-helix." DNA is like two strings twisted together in a long spiral.

Image courtesy U.S. Department of Energy Human Genome Program

DNA is found in all cells as base pairs made of four different nucleotides. Each base pair is formed from two complementary nucleotides bonded together. The four bases in DNA's alphabet are:

Adenine
Cytosine
Guanine
Thymine

Adenine and thymine always bond together as a pair, and cytosine and guanine bond together as a pair. The pairs link together like rungs in a ladder:

Photo courtesy -->Base pairs in DNA bond together to form a ladder-like structure. Because bonding occurs at angles between the bases, the whole structure twists into a helix.

In an E. coli bacterium, this ladder is about 4 million base pairs long. The two ends link together to form a ring, and then the ring gets wadded up to fit inside the cell. The entire ring is known as the genome, and scientists have completely decoded it. That is, scientists know all 4 million of the base pairs needed to form an E. coli bacterium's DNA exactly. The human genome project is in the process of finding all 3 billion or so of the base pairs in a typical human's DNA.


The Big Question

You may remember from a previous section that enzymes are formed from 20 different amino acids strung together in a specific order. Therefore the question is this: How do you get from DNA, made up of only four nucleotides, to an enzyme containing 20 different amino acids? There are two answers to this question:

1)An extremely complex and amazing enzyme called a ribosome reads messenger RNA, produced from the DNA, and converts it into amino-acid chains.
2)To pick the right amino acids, a ribosome takes the nucleotides in sets of three to encode for the 20 amino acids.

What this means is that every three base pairs in the DNA chain encodes for one amino acid in an enzyme. Three nucleotides in a row on a DNA strand is therefore referred to as a codon. Because DNA consists of four different bases, and because there are three bases in a codon, and because 4 * 4 * 4 = 64, there are 64 possible patterns for a codon. Since there are only 20 possible amino acids, this means that there is some redundancy -- several different codons can encode for the same amino acid. In addition, there is a stop codon that marks the end of a gene. So in a DNA strand, there is a set of 100 to 1,000 codons (300 to 3,000 bases) that specify the amino acids to form a specific enzyme, and then a stop codon to mark the end of the chain. At the beginning of the chain is a section of bases that is called a promoter. A gene, therefore, consists of a promoter, a set of codons for the amino acids in a specific enzyme, and a stop codon. That is all that a gene is.

Photo courtesy -->A gene consists of a promoter, the codons for an enzyme and a stop codon. Two genes are shown above. The long strand of DNA in an E. coli bacterium encodes about 4,000 genes, and at any time those genes specify about 1,000 enzymes in the cytoplasm of an E. coli cell. Many of the genes are duplicates.

To create an enzyme, the cell must first transcribe the gene in the DNA into messenger RNA. The transcription is performed by an enzyme called RNA polymerase. RNA polymerase binds to the DNA strand at the promoter, unlinks the two strands of DNA and then makes a complementary copy of one of the DNA strands into an RNA strand. RNA, or ribonucleic acid, is very similar to DNA except that it is happy to live in a single-stranded state (as opposed to DNA's desire to form complementary double-stranded helixes). So the job of RNA polymerase is to make a copy of the gene in DNA into a single strand of messenger RNA (mRNA).

The strand of messenger RNA then floats over to a ribosome, possibly the most amazing enzyme in nature. A ribosome looks at the first codon in a messenger RNA strand, finds the right amino acid for that codon, holds it, then looks at the next codon, finds its correct amino acid, stitches it to the first amino acid, then finds the third codon, and so on. The ribosome, in other words, reads the codons, converts them to amino acids and stitches the amino acids together to form a long chain. When it gets to the last codon -- the stop codon -- the ribosome releases the chain. The long chain of amino acids is, of course, an enzyme. It folds into its characteristic shape, floats free and begins performing whatever reaction that enzyme performs.


No Simple Task

Obviously, the process described on the previous page is not a simple one. A ribosome is an extremely complex structure of enzymes and ribosomal RNA (rRNA) bonded together into a large molecular machine. A ribosome is helped by ATP, which powers it as it walks along the messenger RNA and as it stitches the amino acids together. It is also helped by transfer RNA (tRNA), a collection of 20 special molecules that act as carriers for the 20 different individual amino acids. As the ribosome moves down to the next codon, the correct tRNA molecule, complete with the correct amino acid, moves into place. The ribosome breaks the amino acid off the tRNA and stitches it to the growing chain of the enzyme. The ribosome then ejects the "empty" tRNA molecule so it can go get another amino acid of the correct type.

Photo courtesy -->
1)An RNA polymerase enzyme (yellow) attaches to a DNA strand at a gene's promoter. It then walks down the DNA and creates a copy of it into a strand of messenger RNA (mRNA).
2)The mRNA strand floats free and finds a ribosome.
3)A ribosome (green) attaches to and walks down the mRNA strand to form a chain of amino acids for the enzyme that the gene represents.
4)The amino-acid chain folds into the enzyme's characteristic shape and starts doing its thing.

As you can see, inside every cell there are a variety of processes keeping the cell alive:

1)There is an extremely long and very precise DNA molecule that defines all of the enzymes the cell needs.
2)There are RNA polymerase enzymes attaching to the DNA strand at the starting points of different genes and copying the DNA for the gene into an mRNA molecule.
3)The mRNA molecule floats over to a ribosome, which reads the molecule and stitches together the string of amino acids that it encodes.
4)The string of amino acids floats away from the ribosome and folds into its characteristic shape so it can start catalyzing its specific reaction.

The cytoplasm of any cell is swimming with ribosomes, RNA polymerases, tRNA and mRNA molecules and enzymes, all carrying out their reactions independently of each other.

As long as the enzymes in a cell are active and all of the necessary enzymes are available, the cell is alive. An interesting side note: If you take a bunch of yeast cells and mistreat them (for example, place them in a blender) to release the enzymes, the resulting soup will still do the sorts of things that living yeast cells do (for example, produce carbon dioxide and alcohol from sugar) for some period of time. However, since the cells are no longer intact and therefore are not alive, no new enzymes are produced. Eventually, as the existing enzymes wear out, the soup stops reacting. At this point, the cells and the soup have "died."


Reproduction

The hallmark of all living things is the ability to reproduce. A bacterium reproduction is simply another enzymatic behavior. An enzyme called DNA polymerase, along with several other enzymes that work alongside it, walks down the DNA strand and replicates it. In other words, DNA polymerase splits the double helix and creates a new double helix along each of the two strands. Once it reaches the end of the DNA loop, there are two separate copies of the loop floating in the E. coli cell. The cell then pinches its cell wall in the middle, divides the two DNA loops between the two sides and splits itself in half.

Under the proper conditions, an E. coli cell can split like this every 20 or 30 minutes! The enzymatic process of growing the cell, replicating the DNA loop and splitting happens very rapidly.

For more information, see How Human Reproduction Works.


Poisons and Antibiotics

You can now see that the life of a cell is dependent on a rich soup of enzymes that float in the cell's cytoplasm. Many different poisons work by disrupting the balance of the soup in one way or another.

For example, diphtheria toxin works by gumming up the action of a cell's ribosomes, making it impossible for the ribosome to walk along the mRNA strand. The toxin in a death-cap mushroom, on the other hand, gums up the action of RNA polymerase and halts the transcription of DNA. In both cases, the production of new enzymes shuts down and the cells affected by the toxin can no longer grow or reproduce.

An antibiotic is a poison that works to destroy bacterial cells while leaving human cells unharmed. All antibiotics take advantage of the fact that there are many differences between the enzymes inside a human cell and the enzymes inside a bacterium. If a toxin is found, for example, that affects an E. coli ribosome but leaves human ribosomes unharmed, then it may be an effective antibiotic. Streptomycin is an example of an antibiotic that works in this way.

Penicillin was one of the first antibiotics. It gums up a bacterium's ability to build cell walls. Since bacterial cell walls and human cell walls are very different, penicillin has a big effect on certain species of bacteria but no effect on human cells. The sulfa drugs work by disabling an enzyme that manages the creation of nucleotides in bacteria but not in humans. Without nucleotides, the bacteria cannot reproduce.

You can see that the search for new antibiotics occurs down at the enzyme level, hunting for differences between the enzymes in human and bacterial cells that can be exploited to kill bacteria without affecting human cells.

The unfortunate problem with any antibiotic is that it becomes ineffective over time. Bacteria reproduce so quickly that the probability for mutations is high. In your body, there may be millions of bacteria that the antibiotic kills. But if just one of them has a mutation that makes it immune to the antibiotic, that one cell can reproduce quickly and then spread to other people. Most bacterial diseases have become immune to some or all of the antibiotics used against them through this process.


Viruses

Viruses are absolutely amazing. Although they are not themselves alive, a virus can reproduce by hijacking the machinery of a living cell. The article How Viruses Work describes viruses in detail -- below is a summary.

A virus particle consists of a viral jacket wrapped around a strand of DNA or RNA. The jacket and its short strand of DNA can be extremely small -- a thousand times smaller than a bacterium. The jacket normally is studded with chemical "feelers" that can bond to the outside of a cell. Once docked, the viral DNA (or RNA, depending on the virus) is injected into the cell, leaving the jacket on the outside of the cell.

In the simplest virus, the DNA or RNA strand is now floating freely inside a cell. RNA polymerase transcribes the DNA strand, and ribosomes create the enzymes that the viral DNA specifies. The enzymes that the viral DNA creates are able to create new viral jackets and other components of the virus. In simple viruses, the jackets then self-assemble around replicated DNA strands. Eventually the cell is so full of new viral particles that the cell bursts, freeing the particles to attack new cells. Using this system, the speed at which a virus can reproduce and infect other cells is amazing.

In most cases, the immune system produces antibodies, which are proteins that bind to the viral particles and prevent them from attaching to new cells. The immune system can also detect infected cells by discovering cells decorated with viral jackets, and can kill infected cells.
Antibiotics have no effect on a virus because a virus is not alive. There is nothing to kill! Immunizations work by pre-infecting the body so it knows how to produce the right antibodies as soon as the virus starts reproducing.

See How the Immune System Works for further details.


Genetic Diseases

Many genetic diseases occur because a person is missing the gene for a single enzyme. Here are some of the more common problems caused by missing genes:

1)Lactose intolerance - The inability to digest lactose (the sugar in milk) is caused by a missing lactase gene. Without this gene, no lactase is produced by intestinal cells.

2)Albinism - In albinos, the gene for the enzyme tyrosinase is missing. This enzyme is necessary for the production of melanin, the pigment that leads to sun tans, hair color and eye color. Without tyrosinase, there is no melanin.

3)Cystic fibrosis - In cystic fibrosis, the gene that manufactures the protein called cystic fibrosis transmembrane conductance regulator is damaged. According to Encyclopedia Britannica:

The defect (or mutation) found in the gene on chromosome 7 of persons with cystic fibrosis causes the production of a protein that lacks the amino acid phenylalanine. This flawed protein somehow distorts the movement of salt and water across the membranes that line the lungs and gut, resulting in dehydration of the mucus that normally coats these surfaces. The thick, sticky mucus accumulates in the lungs, plugging the bronchi and making breathing difficult. This results in chronic respiratory infections, often with Staphylococcus aureus or Pseudomonas aeruginosa. Chronic cough, recurrent pneumonia, and the progressive loss of lung function are the major manifestations of lung disease, which is the most common cause of death of persons with cystic fibrosis.


Other genetic diseases include Tay-Sachs disease (damage to the gene for the enzyme hexosaminidase A leads to an accumulation of a chemical in the brain that destroys it), sickle cell anemia (improper coding of the gene that produces hemoglobin), hemophilia (lack of a gene for a blood-clotting factor) and muscular dystrophy (caused by a defective gene on the X chromosome). There are something like 60,000 genes in the human genome, and over 5,000 of them, if damaged or missing, are known to lead to genetic diseases. It is amazing that damage to just one enzyme can lead, in many cases, to life-threatening or disfiguring problems.


Biotechnology


So what is biotechnology and genetic engineering? There are three major developments that act as the signature of biotech, with many more surprises coming down the road:

1)Bacterial production of substances like human interferon, human insulin and human growth hormone. That is, simple bacteria like E. coli are manipulated to produce these chemicals so that they are easily harvested in vast quantities for use in medicine. Bacteria have also been modified to produce all sorts of other chemicals and enzymes.

2)Modification of plants to change their response to the environment, disease or pesticides. For example, tomatoes can gain fungal resistance by adding chitinases to their genome. A chitinase breaks down chitin, which forms the cell wall of a fungus cell. The pesticide Roundup kills all plants, but crop plants can be modified by adding genes that leave the plants immune to Roundup.

3)Identification of people by their DNA. An individual's DNA is unique, and various, fairly simple tests let DNA samples found at the scene of a crime be matched with the person who left it. This process has been greatly aided by the invention of the polymerase chain reaction (PCR) technique for taking a small sample of DNA and magnifying it millions of times over in a very short period of time. To understand some of the techniques used in biotechnology, lets look at how bacteria have been modified to produce human insulin.

Insulin is a simple protein normally produced by the pancreas. In people with diabetes, the pancreas is damaged and cannot produce insulin. Since insulin is vital to the body's processing of glucose, this is a serious problem. Many diabetics, therefore, must inject insulin into their bodies daily. Prior to the 1980s, insulin for diabetics came from pigs and was very expensive.

To create insulin inexpensively, the gene that produces human insulin was added to the genes in a normal E. coli bacteria. Once the gene was in place, the normal cellular machinery produced it just like any other enzyme. By culturing large quantities of the modified bacteria and then killing and opening them, the insulin could be extracted, purified and used very inexpensively.

The trick, then, is in getting the new gene into the bacteria. The easiest way is to splice the gene into a plasmid -- a small ring of DNA that bacteria often pass to one another in a primitive form of sex. Scientists have developed very precise tools for cutting standard plasmids and splicing new genes into them. A sample of bacteria is then "infected" with the plasmid, and some of them take up the plasmid and incorporate the new gene into their DNA. To separate the infected from the uninfected, the plasmid also contains a gene giving the bacteria immunity to a certain antibiotic. By treating the sample with the antibiotic, all of the cells that did not take up the plasmid are killed. Now a new strain of insulin-producing E. coli bacteria can be cultured in bulk to create insulin.

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Related:
http://gonashgo.blogspot.com/2009/01/435a-collection-of-posts-about-life.html


Quotes of Aga Khan IV and Others:

"Islamic doctrine goes further than the other great religions, for it proclaims the presence of the soul, perhaps minute but nevertheless existing in an embryonic state, in all existence in matter, in animals, trees, and space itself. Every individual, every molecule, every atom has its own spiritual relationship with the All-Powerful Soul of God"(Memoirs of Aga Khan III, 1954)

"In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

"The second great historical lesson to be learnt is that the Muslim world has always been wide open to every aspect of human existence. The sciences, society, art, the oceans, the environment and the cosmos have all contributed to the great moments in the history of Muslim civilisations. The Qur’an itself repeatedly recommends Muslims to become better educated in order better to understand God’s creation"(Closing Address by His Highness Aga Khan IV at the "Musée-Musées" Round Table Louvre Museum, Paris, France, October 17th 2007)

"....in Islam, but particularly Shia Islam, the role of the intellect is part of faith. That intellect is what seperates man from the rest of the physical world in which he lives.....This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives. Of that I am certain"(Aga Khan IV, Dar-es-Salaam, Tanzania, August 17th 2007)

"Of the Abrahamic faiths, Islam is probably the one that places the greatest emphasis on knowledge. The purpose is to understand God's creation, and therefore it is a faith which is eminently logical. Islam is a faith of reason"(Aga Khan IV, Spiegel Magazine interview, Germany, Oct 9th 2006)

"Our interpretation of Islam places enormous value on knowledge. Knowledge is the reflection of faith if it is used properly. Seek out that knowledge and use it properly"(Aga Khan IV, Toronto, Canada, 8th June 2005)

"A thousand years ago, my forefathers, the Fatimid imam-caliphs of Egypt, founded al-Azhar University and the Academy of Knowledge in Cairo. In the Islamic tradition, they viewed the discovery of knowledge as a way to understand, so as to serve better God's creation, to apply knowledge and reason to build society and shape human aspirations"(Aga Khan IV, Speech, 25th June 2004, Matola, Mozambique.)

"In this context, would it not also be relevant to consider how, above all, it has been the Qur'anic notion of the universe as an expression of Allah's will and creation that has inspired, in diverse Muslim communities, generations of artists, scientists and philosophers? Scientific pursuits, philosophic inquiry and artistic endeavour are all seen as the response of the faithful to the recurring call of the Qur'an to ponder the creation as a way to understand Allah's benevolent majesty. As Sura al-Baqara proclaims: 'Wherever you turn, there is the face of Allah'.The famous verse of 'light' in the Qur'an, the Ayat al-Nur, whose first line is rendered here in the mural behind me, inspires among Muslims a reflection on the sacred, the transcendent. It hints at a cosmos full of signs and symbols that evoke the perfection of Allah's creation and mercy"(Aga Khan IV,Speech, Institute of Ismaili Studies, October 2003, London, U.K.)

"In sum the process of creation can be said to take place at several levels. Ibda represents the initial level - one transcends history, the other creates it. The spiritual and material realms are not dichotomous, since in the Ismaili formulation, matter and spirit are united under a higher genus and each realm possesses its own hierarchy. Though they require linguistic and rational categories for definition, they represent elements of a whole, and a true understanding of God must also take account of His creation. Such a synthesis is crucial to how the human intellect eventually relates to creation and how it ultimately becomes the instrument for penetrating through history the mystery of the unknowable God implied in the formulation of tawhid."(Azim Nanji, Director, Institute of Ismaili Studies, London, U.K., 1998)

"Education has been important to my family for a long time. My forefathers founded al-Azhar University in Cairo some 1000 years ago, at the time of the Fatimid Caliphate in Egypt. Discovery of knowledge was seen by those founders as an embodiment of religious faith, and faith as reinforced by knowledge of workings of the Creator's physical world. The form of universities has changed over those 1000 years, but that reciprocity between faith and knowledge remains a source of strength"(Aga Khan IV, 27th May1994, Cambridge, Massachusets, U.S.A.)

"An institution dedicated to proceeding beyond known limits must be committed to independent thinking. In a university scholars engage both orthodox and unorthodox ideas, seeking truth and understanding wherever they may be found. That process is often facilitated by an independent governance structure, which serves to ensure that the university adheres to its fundamental mission and is not pressured to compromise its work for short-term advantage. For a Muslim university it is appropriate to see learning and knowledge as a continuing acknowledgement of Allah's magnificence"(Aga Khan IV, Speech, 1993, Aga Khan University, Karachi, Pakistan)

"The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims. Exchanges of knowledge between institutions and nations and the widening of man's intellectual horizons are essentially Islamic concepts. The Faith urges freedom of intellectual enquiry and this freedom does not mean that knowledge will lose its spiritual dimension. That dimension is indeed itself a field for intellectual enquiry. I can not illustrate this interdependence of spiritual inspiration and learning better than by recounting a dialogue between Ibn Sina, the philosopher, and Abu Said Abu -Khyar, the Sufi mystic. Ibn Sina remarked, "Whatever I know, he sees". To which Abu Said replied," Whatever I see, he knows"."(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11th 1985)

“Muslims believe in an all-encompassing unit of man and nature. To them there is no fundamental division between the spiritual and the material while the whole world, whether it be the earth, sea or air, or the living creatures that inhabit them, is an expression of God’s creation.”(Aga Khan IV, University of Virginia, Charlottesville, Virginia, USA, 13 April 1984)

"In Islamic belief, knowledge is two-fold. There is that revealed through the Holy Prophet (s.a.s.) and that which man discovers by virtue of his own intellect. Nor do these two involve any contradiction, provided man remembers that his own mind is itself the creation of God. Without this humility, no balance is possible. With it, there are no barriers. Indeed, one strength of Islam has always lain in its belief that creation is not static but continuous, that through scientific and other endeavours, God has opened and continues to open new windows for us to see the marvels of His creation"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"Our religious leadership must be acutely aware of secular trends, including those generated by this age of science and technology. Equally, our academic or secular elite must be deeply aware of Muslim history, of the scale and depth of leadership exercised by the Islamic empire of the past in all fields"(Aga Khan IV, 6th February 1970, Hyderabad, Pakistan)

"Thus Islam's basic principle can only be defined as mono-realism and not as monotheism. Consider, for example, the opening declaration of every Islamic prayer: "Allah-o-Akbar". What does that mean? There can be no doubt that the second word of the declaration likens the character of Allah to a matrix which contains all and gives existence to the infinite, to space, to time, to the Universe, to all active and passive forces imaginable, to life and to the soul. Imam Hassan has explained the Islamic doctrine of God and the Universe by analogy with the sun and its reflection in the pool of a fountain; there is certainly a reflection or image of the sun, but with what poverty and with what little reality; how small and pale is the likeness between this impalpable image and the immense, blazing, white-hot glory of the celestial sphere itself. Allah is the sun; and the Universe, as we know it in all its magnitude, and time, with its power, are nothing more than the reflection of the Absolute in the mirror of the fountain"(Memoirs of Aga Khan III, 1954)

"Islam is fundamentally in its very nature a natural religion. Throughout the Quran God's signs (Ayats) are referred to as the natural phenomenon, the law and order of the universe, the exactitudes and consequences of the relations between natural phenomenon in cause and effect. Over and over, the stars, sun, moon, earthquakes, fruits of the earth and trees are mentioned as the signs of divine power, divine law and divine order. Even in the Ayeh of Noor, divine is referred to as the natural phenomenon of light and even references are made to the fruit of the earth. During the great period of Islam, Muslims did not forget these principles of their religion. Alas, Islam which is a natural religion in which God's miracles are the very law and order of nature drifted away and is still drifting away, even in Pakistan, from science which is the study of those very laws and orders of nature.……Islam is a natural religion of which the Ayats are the universe in which we live and move and have our being………..The God of the Quran is the one whose Ayats are the universe……"(Aga Khan III, April 4th 1952)

"Nature is the great daily book of God whose secrets must be found and used for the well-being of humanity"(Aga Khan III, Radio Pakistan, Karachi, Pakistan, February 19th 1950)

"In fact this world is a book in which you see inscribed the writings of God the Almighty"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet)

"O brother! You asked: What is the [meaning of] `alam [world] and what is that entity to which this name applies? How should we describe the world in its entirety? And how many worlds are there? Explain so that we may recognize. Know, O brother, that the name `alam is derived from [the word] `ilm(knowledge), because the traces of knowledge are evident in [all] parts of the physical world. Thus, we say that the very constitution (nihad) of the world is based on a profound wisdom"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet, from his book "Knowledge and Liberation")

“The physician considers [the bones] so that he may know a way of healing by setting them, but those with insight consider them so that through them they may draw conclusions about the majesty of Him who created and shaped [the bones]. What a difference between the two who consider!”(Abu Hamid Al-Ghazali, Muslim Theologian-Philosopher-Mystic, d1111CE)

"Tarkib' is composition as in the compounding of elements in the process of making more complex things, that is, of adding together two things to form a synthesis, a compound. Soul composes in the sense of 'tarkib'; it is the animating force that combines the physical elements of the natural universe into beings that move and act. Incorporating is an especially apt word in this instance. It means to turn something into a body, as in 'composing'. But it is actually the conversion of an intellectual object, a thought, into a physical thing. Soul acts by incorporating reason into physical objects, the natural matter of the universe and all the things composed of it"(Abu Yakub Al-Sijistani,10th century Fatimid Ismaili cosmologist, d971CE, from the book, 'Abu Yakub Al-Sijistani: Intellectual Missionary', by Paul Walker)

"Every particle of the Creation has a share of the Command of God, because every creature shares a part of the Command of God through which it has come to be there and by virtue of which it remains in being and the light of the Command ofGod shines in it. Understand this!"(Abu Yakub Al Sijistani, 10th century Fatimid Ismaili cosmologist, d971, Kashf al-Mahjub("Unveiling of the Hidden"))

"According to a famous hadith of the Prophet Muhammad: The first(and only) thing created by God was the Intellect ('aql)"(circa 632CE)

"Seek knowledge from the cradle to the grave"(Prophet Muhammad, circa 632CE)

"One hour of contemplation on the works of the Creator is better than a thousand hours of prayer"(Prophet Muhammad, circa 632CE)

"The ink of the scholar is better than the blood of the martyr"(Prophet Muhammad, circa 632CE)

"All human beings, by their nature, desire to know."(Aristotle, The Metaphysics, circa 322BC)

The above are 28 quotes and excerpts taken from Blogpost Four Hundred, a collection of around 100 quotes on the subjects of Knowledge, Intellect, Creation, Science and Religion:
http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html



Easy Nash

The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)

497)Professor Arif Babul In Conversation With Blogger Simerg:On Science Funding, Muslim Scientists, An Ismaili Academy;Quotes of Aga Khans And Others.

SCIENCE FUNDING
Simerg: You have mentioned about the importance of funding basic research in science, as opposed to only paying attention to the applied fields. Many people seem to have a misperception that “basic science” is entirely self-contained, and that it confers no tangible benefit to society. Could you reflect on this sentiment, and discuss why you feel investment in basic science is so important?

Dr. Babul: It is true that most people harbour the misconception that basic science confers no benefit to society, that it is purely a curiousity-driven endeavour, and the latter is true to some extent but the “no benefit” idea is definitely wrong.

Let me explain: If you ask me why I do what I do, I do it because I just want to understand and to know. I really don’t think about application of knowledge that I create. But on the other hand, when you step back and look back at the developments in science over a fifteen-twenty year window, it becomes clear that most of the technological revolutions of the past two hundred years have occurred as a direct result of major conceptual breakthroughs that emerged from basic research. On the average, the estimate of the annual rate of return on investment in basic research ranges from 28% to 50%. In the case of astronomy, for example, for every dollar that the Government commits to research, the return to the economy has been estimated to ten dollars.

Let me give you a specific example of how this works. If you look at the sky, the reason why stars look like they’re twinkling is because as light passes through our atmosphere, which is moving, it bends, and when you see this light bending, it seems like the star is moving, which gives it its twinkling effect.

…..when you step back and look back at the developments in science over a fifteen-twenty year window, it becomes clear that most of the technological revolutions of the past two hundred years have occurred as a direct result of major conceptual breakthroughs that emerged from basic research.

For astronomers, twinkling is an irritation because it smears out the light, and you want the sharpest image possible. What somebody figured out was that if I take a laser beam and shine it from the ground up, a part of the atmosphere lights up so I see a dot in the sky. I know that the dot should be absolutely round and sharp, but because the atmosphere is moving, it doesn’t look round and sharp. So I point a telescope at that dot, and program a computer to alter the shape of the telescope optics so that the image of the dot is perfectly sharp. In this way, the telescope is calibrated to account for the so-called “twinkling effect,” and now all the stars and galaxies in the vicinity of the laser dot will appear extremely sharp.

You’re probably thinking in the back of your mind, “So what?”

Well, a few years ago, the Optometry school in Waterloo sent some of its researchers to the Herzberg Institute of Astrophysics in Victoria; they wanted to learn about these technologies. It turns out that when optometrists look in your eye and try to image the retina, they have to look through all that fluid in your eye, and the fluid is moving, and that moving fluid distorts the image of the retina. But the same technology that allows astronomers to correct for the atmospheric distortions can also correct for the distortions due to the moving fluid in the eye resulting in pictures of the back of your eye that are perfectly sharp. And the sharper the picture, the earlier you can detect diseases of the eye such as glaucoma and even signs of diabetes. So in a secondary way, innovative new technology has been introduced into the health system.

Let me give you one other very quick example. As early as 1917, Albert Einstein had described the theory of stimulated emission but it took 30 years before physicists, motivated by successes in developing masers (microwave amplification by stimulated emission of radiation) figured out how to make lasers. Initially, nobody could figure out what to do with a laser. It was dubbed “a solution looking for a problem.” Today, 30 years later, the laser is at the heart of virtually all high-tech devices we use, from DVD and CD players to supermarket bar code scanners and laser scalpels for surgery. Laser light is even used to transmit telephone calls and internet signals.

The laser, deemed useless in the past, is now present in countless technological devices.
So you can ask the question, “did the inventor of the laser, in his wildest imagination and dreams, anticipate that laser would turn out to be so useful?” The answer is no but others did and they turned it into a versatile, highly useful, even indispensible tool. Still, Einstein, deserves the credit for providing the conceptual spark, as do the individuals responsible for the pushing ahead with the first laser device. In the same vein, basic scientists are people who sometime purposefully, sometime accidentally provide the all-important sparks, sparks without which the fires of innovation would never get started.


MUSLIM SCIENTISTS
Simerg: When you look back at Islamic history, which Islamic scientists are your inspirations?

Dr. Babul: The two people that stand out in my mind are Ibn al-Haytham and Nasir Al-Din Al-Tusi. Al-Haytham worked at the Dar al-Ilm in Cairo under the patronage of Imam al-Hakim. He was given a stipend – a sort of a “research grant” and did groundbreaking work in the area of optics. It is only over the past few years that his contributions to the field of optics have started to be recognized and he is increasingly referred to the “father of optics.” I seem to recall somewhere that Newton acknowledged his debt to Al-Haytham.

…..Al-Haytham was in the vanguard, resisting a growing movement within the Muslim world at the time to try and limit the scope of scientific discoveries….Dogmatism, which was always present but kept in check, was beginning to spread, and if your scientific work was not quite in consonance with “accepted” interpretations of the Qur’an, you would come under pressure to abandon your work….He believed that nature too is God’s Book; God commands us in the Qur’an to go out and understand it, and that’s exactly what we should do.

Al-Haytham was also one of the pioneers of what we today call the “scientific method” because he was a strong proponent of empirical tests of scientific theories. He was one of the earliest scholars who argued that to understand nature, one must study nature firsthand. And if the observations and experiments say that something is untrue, then we have to accept that our preconceptions are not quite right. Observation must take supremacy over our ideology or myth. That is also a foundation of modern science method: You test your ideas, and reject them if nature rejects them. Contemporary scientists like to say, “Man proposes, Nature disposes.” The kernel of that idea were already present in Ibn Al-Haytham’s work.

Picture:
A facsimile frontispiece from a 1572 Latin edition of ‘Optics,’ the magnum opus of 11th century mathematician al-Hasan ibn al-Haytham (Alhazen), who pioneered modern scientific concepts of vision. Courtesy of Houghton Library

In keeping with the above approach, Al-Haytham was in the vanguard, resisting a growing movement within the Muslim world at the time to try and limit the scope of scientific discoveries based on interpretations of the Qur’an. Dogmatism, which was always present but kept in check, was beginning to spread, and if your scientific work was not quite in consonance with “accepted” interpretations of the Qur’an, you would come under pressure to abandon your work.

Al-Haytham was an active opponent of that approach. He believed that nature too is God’s Book; God commands us in the Qur’an to go out and understand it, and that’s exactly what we should do. And in his writings he was already trying to establish that if there are tensions between these two areas, we should acknowledge that nature, as a book of God, is worthy of study in its own right and on its own terms. So in many ways Ibn Al-Haytham was a dramatic figure, and unique too.

Simerg: And how about Tusi?

Dr. Babul: Tusi was influenced by al-Haytham, and carried on his legacy. In doing so, he laid down many of the foundational ideas, particularly the mathematical ones, for the study of the solar systems, which allowed Copernicus to develop his heliocentric model. In fact in Tusi’s own model, it was straightforward to exchange Sun for the Earth as the center of the solar system because the mathematics was already there. And I’ve often wondered why it was that Tusi did not consider the possibility.

A drawing by the Alamut astronomer Nasir Al-Din Tusi, illustrates what's now known as a Tusi-couple, used to depict an aspect of planetary motion that Ptolemy described in his convoluted equant theory. Together with its clarity, and the elegance of the Arabic script, it combines calligraphic elements that exemplify good solid graphic design principles still in place.
I remember talking to a scholar who has studied Tusi’s writing extensively, and he mentioned that in some of Tusi’s writings, it’s hinted that he actually did think about it, and asked the question, “what if the earth was moving?” In fact, I have since learnt that a several other Muslim astronomers considered the possibility but at the end of the day, they concluded that this model offered no advantage. Tusi tried to test the idea. If the earth was moving, he expected the positions of the stars to change over the course of a year, but he couldn’t see the change in the positions of the stars, so he decided that the earth was not moving. And that’s an interesting argument, because to detect the changes in the positions of the stars, he would have needed a telescope, which was three or four hundred years into the future.

So it was interesting that he was far ahead of his time in terms of thinking, but being a good scientist he rejected the idea on the basis that he did not have the empirical evidence to support it.


ISLAMIC ERA: SCIENCE TIMELINE(Timeline compiled by Blogger Simerg; Nature magazine was used as a reference for some of the material above)

c. 750-1258 Abbasid Era.

c756-929 Umayyads rule over Spain
The Abbasids overthrew the Umayyad caliphate, which had spread Islam through Asia, the Middle East, North Africa and the Iberian peninsula. The Abbasids moved the caliphate’s capital from Damascus to Baghdad. Umayyads, however, retain control over the Iberian territories. This was a particularly productive period for science in Islamic history.

c. Late 700s Muhammad al-Farabi
Al-Farabi lived during the time of first Abbasid Caliph Al-Mansur and is credited to have built the first astrolabe in the Islamic world. Along with his father and Yaqub ibn Tariq, he helped translate the Indian astronomical text by Brahmagupta (fl. 7th century), the Brahmasphutasiddhanta, into Arabic as Az-Zīj ‛alā Sinī al-‛Arab, or the Sindhind. He lived at the beginning of the concerted effort, involving Christian, Jewish, Hindu, Zoroastrian and even Sabian scholars, to translate Greek and Hindu works into Arabic.

c. 721-813 Jabir ibn Hayyan
Works attributed to this alchemist had lasting influence in Europe until the sixteenth century. He is credited, for example, with introducing a completely new approach – controlled, systematic experimentation – that has since become a hallmark of contemporary science’s empirical effort. Many words in chemistry have Arabic roots including alkali (al-qaliy) and alcohol (al-kohl). Jabir is believed to have been an apprentice of Ja’far al-Sadiq.

c. 813 Abbasid Caliph al-Mamun
One of the great patrons of intellectual inquiry in Islamic history and in due course, establishes the House of Wisdom.

c. 830-1258 House of Wisdom, Baghdad
Activities at this library and research centre included translation of Greek works into Arabic by both Muslim and non-Muslim scholars. Free public libraries later spread to other cities.

c. 780-840 Al-Khwarizmi
Mathematician who gave his name to ‘algorithm’ and promoted the use of Indian numerals. Latin translations of his books introduced algebra (derived from al-jabr) to Europe.

c. 850 Banu Musa brothers
Published their first book of ingenious mechanical devices. Examples include fountains that change shape by the minute, clocks with all sort of gimmicks and contraptions, flutes that play by themselves, water jugs that serve drinks automatically, and even a full-sized mechanical tea girl that actually serves tea!

c. 875 Ibn Firnas
Iberian scientist, constructs a hang-glider from silk and eagle feathers on a wooden frame and successfully floated in the air, circling for up to ten minutes, before gradually crash-landing. It was only later, he realized that birds use their tails to slow down before landing.

c. 865-926 Al-Razi (Rhazes)
Persian who contributed to medicine, alchemy and philosophy. He formulated the first known description of smallpox, which the Ancient Greeks had confused with measles.

c. 909-1171 Fatimid Era
The Fatimid Caliphate was an Ismaili Shi’a dynasty that ruled over varying areas of the Maghreb, Egypt, Sicily, Malta and the Levant from 5 January 909 to 1171. Along with the Abbasids, the Fatimid period represents one of the greatest eras in Islamic history. Fatimids patronized intellectual activies and created major libraries and Cairo, their capital city(founded in 969), grew into a centre of scholarship and science. The Fatimid intellectual activities centred around two institutions: al-Azhar and Dar al-Ilm.

c. 988 al-Azhar
Established in the time of Caliph al-Muizz, the Fatimid Caliph who built Cairo, al-Azhar is the Fatimids’ most famous legacy and is often described as the world’s oldest fully-functioning institutions of teaching and scholarship. al-Azhar was concerned mainly with religious sciences and related studies, including jurisprudence.

c. 996 Fatimid Caliph al-Hakim
al-Hakim becomes Caliph at the age of 11. In due course, he establishes a unique centre of excellence for teaching and research known as Dar al-Ilm (House of Knowledge).Fatimid-era intellectual scholarship and pursuits reached their zenith during the reign of al-Hakim. Louis Massignon,the renowned French Orientalist, has designated the 11th century as the Ismaili Century of Islam.

c. 1005 Dar al-Ilm
Dar al-Ilm was founded by Caliph al-Hakim in 1005. Dar al-lm was the first institution of its kind. It drew together research and teaching of a wide variety of subjects such as medicine, astronomy, mathematics, philology, logic, law and like, under a single “roof”. The scholars, teachers and the librarians were supported by an endowment – the first known record of an institution of research and teaching being supported in this fashion – and scholars who achieved high standards were awarded with robes of honour, much like today’s universities award degrees and gowns.Additionally, the Dar al-Ilm housed one of the largest, most extensive libraries in the world (at the time).

c. 965-1039 Ibn al- Haytham (Alhazen)
Basra-born Fatimid polymath researcher, and one of the most brilliant of all Islamic scholars, who lived in Cairo in the time of Caliph al-Hakim, al-Haytham made significant contributions to the principles of optics, as well as to anatomy, astronomy, engineering, mathematics, medicine, ophthalmology, philosophy, physics, psychology, and visual perception. He is credited with refuting Greek models of vision using “controlled experiments” and arguing instead that vision is the result of images being formed in the eye. He also developed the basics of the camera obscura. Due his foundational work in optics, al-Haytham is often referred to as the “father of optics”. Due to his formulation of a modern quantitative and empirical approach to physics and science, and especially the central role of experimentation and observations as the only legitimate way to arbitrate between competing explanations, he is also acknowledged as the pioneer of the modern scientific method.

c. 973-1048 Abu Rayhan al-Biruni
A brilliant Persian polymath of the 11th century, al-Biruni was a scientist and physicist, an anthropologist and comparative sociologist, an astronomer and chemist, a critic of alchemy and astrology, an encyclopedist and historian, a geographer and traveler, a geodesist and geologist, a mathematician, a pharmacist and psychologist, an Islamic philosopher and theologian, and a scholar and teacher. He was the first Muslim scholar to study India and the Brahminical tradition. Like al-Haytham, he was one of the earliest exponents of the experimental scientific method, and was responsible for introducing the experimental method into mechanics. He was one of the first Islamic astronomers to seriously consider the possibility that the earth orbited the sun (as we now hold today) than the other way around. George Sarton, the father of the history of science, described Biruni as “one of the very greatest scientists of Islam, and, all considered, one of the greatest of all times.”

c. 980-1037 Ibn Sina (Avicenna)
Persian physician and philosopher born in an Ismaili family from Bukhara. The Latin translation of his Al-Qanun fi al-Tibb (The Canon of Medicine) was a highly regarded medical text in Europe until the sixteenth century.

c 1090 – 1256 Alamut Library
Following a schism, the the Nizari Ismailis established a state centred on the fortress of Alamut. In keeping with their traditions, the Ismaili leadership maintained a sophisticated outlook and placed a high value on intellectual activities. They created impressive libraries of which the library at the fortress of Alamut was the most famous. The Alamut library contained not only important collections of religious and philosophical texts, but also scientific treatises and instruments. Among the eminent Muslim scholars who availed themselves of the patronage of the Ismaili rulers (and access to their libraries) during time was Nasiral-Din al-Tusi, who spent three decades with the Ismailis.

c. 1126-1198 Ibn Rushd (Averroës)
Spanish-born Islamic philosopher who tried to reconcile the contradictions between Aristotelian ideas of studying nature through observation and reason, and religious truth. His writings and translations had considerable influence in Europe.

c. 1201-1274 Nasir al-Din al-Tusi
Persian astronomer, mathematician and astronomer who worked under Ismaili patrons in various centers including at Alamut Fortress. He established the Maragha Observatory and introduced several mathematical devices, including the ‘Tusi couple”, that Islamic scholars to greatly improve ptolomeic models of planetary motion. The “Tusi couple” as well mathematical models for planetary motion by Tusi’s student, Mo’ayyeduddin Urdi, was instrumental in Copernicus’s reformulation of the solar system where planets revolve around the sun (see also Al-Shatir below).

c. 1259- c.1304 Maragha Observatory
One of the top three observatories in the Islamic world, this was built in Maragha in modern-day Iran. Maragha had a library of 400,000 books and a school of astronomy.

c. 1213-1288 Ibn al-Nafis
Damascus-born physician who worked in Cairo hospitals and produced the first recorded explanation of the blood leaving the heart for the lungs. William Harvey’s discovered the full pulmonary cycle in the 1600’s.

c. 1281-1923 Ottoman Era
The Ottoman Empire spread from Anatolia into north Africa, Asia, the Middle East, and eastern and southern Europe.

c. 1284 Al-Mansuri / Qalawun hospital, Cairo
Specialized institutions that treated disease for free and conducted research took root under Islamic rule, building on Roman efforts. The hospitals in Cairo and in Baghdad had wards for different illnesses. Clinicians took detailed case notes, which were collated into teaching manuals.

c. 1304-1375 Ibn al-Shatir
Damascus-born astronomer and mathematician who developed new models of the Moon and planetary motion that eliminated problems with Greek models. Aspects of his work are identical to that produced by Copernicus.

c. 1332-1406 Ibn Khaldun
Ibn Khaldūn born in North Africa in present-day Tunisia. is considered a forerunner of several social scientific disciplines: demography, cultural history, historiography,the philosophy of history, and sociology.While he is considered one of the forerunners of modern economics, he is preceded by the Indian scholar-philosopher Chanakya.He is considered by many to be the father of a number of these disciplines, and of social sciences in general, for anticipating many elements of these disciplines centuries before they were founded in the West. He is best known for his Muqaddimah (known as Prolegomenon in the West).

Timeline compiled by Simerg; Nature magazine was used as a reference for some of the material above

Continue at the Source:
http://simerg.com/about/voices-babul-on-science-funding-muslim-scientists-intelligent-design-and-neurosciences/


"ISMAILI ACADEMY"
Simerg: What are your hopes and aspiration for the Jamat in Canada, with the talent that we have?

Babul: Apart from my concerns as a father, I also see the present time as time of opportunity for the Ismaili community in the West. We have been in Canada nearly 40 years now. And during this time, I think that members of the Jamat have done extremely well in terms of achieving professional and entrepreneurial successes. By and large, this has been an individual effort and I think now is the time to convert these individual successes into collective assets for the community.

Focusing on Ismailis in academia, I wouldn’t be surprised if there are Ismaili professors in nearly every area of study. I personally know Ismaili Professors of Art History, Ismaili Professors of Mathematics, Ismaili Professors of Engineering, of Law, of Islamic Studies, of Physics. We have researchers pursuing careers in molecular biology, in neuroscience…the list just goes on and on.
And these individuals are at the forefront in their own fields – truly stellar individuals. And what gives me great optimism is that there is cadre of brilliant graduate students moving in the same direction, and probably many more interested undergraduate and high school students.

With this in mind, two years ago, I started toying with the idea of setting up something that I like to call the “Ismaili Academy”, a “tent structure” that would bring together all the Ismaili academics from around the world.

Academics possess skills which transcend their own specific area of expertise; they bring unique ways of thinking about and formulating responses to critical challenges facing the Jamat. It is not a coincidence that government think tanks often include academics that have no direct expertise or relationship to the issue that the think tank is meant to consider. And so the Academy would be a resource for the leadership to draw on. It would offer the leadership an up-to-date snapshot of the expertise and talent that is available.

Second, the Ismaili Academy would provide a forum whereby junior members of the academia can seek guidance and advice from more senior members, and where senior members can pass down their insights and experiences to the next generation so that the latter can avoid pitfalls. I see no reason why we, as a community, cannot be proactive in giving the next generation a career boost. It is one of many ways of ensuring that the impact of the community continues to grow in the years to come.

Academics possess skills which transcend their own specific area of expertise; they bring unique ways of thinking about and formulating responses to critical challenges facing the Jamat. It is not a coincidence that government think tanks often include academics that have no direct expertise or relationship to the issue that the think tank is meant to consider. And so the Academy would be a resource for the leadership to draw on.

Even high school and university students could benefit from such an infrastructure. Consider, for example, students wishing to pursue a career in science. There are summer research positions, scholarships and fellowships they should be applying for to enhance their profiles. Many of these are not widely announced, but those of us who have been in the system often come across these and can bring them to the attention of interested students.

I think the real difficulty here is figuring out how get this Academy idea going, and how to get enough momentum behind that idea so that it could actually come to fruition. It definitely requires institutional assistance; you can’t do something that involves the community without the direct support from the institutions, so that’s where I am.

I’m at the stage of working with different members of the leadership trying to see how we could bring this about. It is, after all, very much in keeping with the idea of cooperatives and associations that Hazar Imam mentioned over the Golden Jubilee Year.

Simerg: Most of your life has been dedicated toward trying to understand the mechanisms and complexities of this incredible Universe of ours, through Allah’s greatest gift to mankind – the intellect. His Highness the Aga Khan once said and I quote: “The Divine intellect both transcends and informs the human intellect.” What does this statement hold for you – say when you are totally engrossed in your field of study, and you come across discoveries that you make, or formulae that you develop. How do you relate this to the Divine Intellect? Is the discovery something that you attribute to Allah’s blessing?

Dr. Babul: I definitely see it as a blessing.
A few of my colleagues have written about these experiences, when you’re struggling with problems and then out of the blue something just hits you. In those kinds of moments, you often literally lose yourself and are transported into a different time and space, if you will.
I feel that those moments are as spiritual as any other moments that are traditionally associated with religious experiences. And it goes back to what I was saying earlier: I don’t divide up my world. I don’t become an Ismaili Muslim only during prayer time. I am an Ismaili Muslim 24/7, and my relationship to the world around me is informed by this notion of an all-pervasive “Divine” or “Mystery.”

I exist in this Mystery, I try and guide my actions by an ethical system that is informed by it – [laughing] can’t say I am altogether successful in this – and so I’m fortunate that once in a while the door will open and I’ll get the sense of it through my work. I really see it as one of a variety of spiritual experience.

The phrase I would prefer to use is “a glimpse of Mystery.” When we think of the Divine, we tend to narrow it and compartmentalize it, but that’s not the case. Mawlana Sultan Muhammad Shah, again, said, “you live in it, you breathe in it, you are immersed in it.” So every aspect of your life is directly related to and informed by this.

I don’t divide up my world. I don’t become an Ismaili Muslim only during prayer time. I am an Ismaili Muslim 24/7, and my relationship to the world around me is informed by this notion of an all-pervasive “Divine” or “Mystery.”

And I don’t think you have to be a scientist to experience those precious moments, those “glimpses of Mystery.” It could happen while reading poetry, or during the act of creating sculpture or a painting. It could even happen during an everyday moment. Imagine spending every evening on a beach, watching the sunset. Most of the days, you don’t pay much attention to this, or it doesn’t strike you as particular moving. Then one day, as the sun sinks below the horizon, you are struck by the brilliant colours, you are mesmerized, and you forget where and who you are. You’re just caught. I would say that you’ve just had a spiritual experience.
And this is when you’d say, “Masha’Allah.”

Simerg: Thank you Professor Babul. It has been immensely rewarding talking with you.

Continue at the Source:
http://simerg.com/about/voices-babul-aspirations-for-the-family-and-the-jamat-an-ismaili-academy-family-pursuits-the-frontierless-brotherhood-and-allahs-blessing/

Link to all 4 parts of the interview:
http://gonashgo.blogspot.com/2009/06/485a-magnificently-detailed-interview.html

http://ismailimail.wordpress.com/2009/06/08/astrophysicist-scientist-dr-arif-babul-in-conversation-with-simerg/

http://ismailimail.wordpress.com/2009/06/22/astrophysicist-scientist-dr-arif-babul-in-conversation-with-simerg-parts-ii-iii-and-iv/

http://ismailimail.wordpress.com/2009/06/13/part-2-of-interview-with-astrophysicist-scientist-dr-arif-babul/



Quotes of Aga Khans and Others:

".....As we use our intellect to gain new knowledge about Creation, we come to see even more profoundly the depth and breadth of its mysteries. We explore unknown regions beneath the seas – and in outer space. We reach back over hundreds of millions of years in time. Extra-ordinary fossilised geological specimens seize our imagination – palm leaves, amethyst flowers, hedgehog quartz, sea lilies, chrysanthemum and a rich panoply of shells. Indeed, these wonders are found beneath the very soil on which we tread – in every corner of the world – and they connect us with far distant epochs and environments.
And the more we discover, the more we know, the more we penetrate just below the surface of our normal lives – the more our imagination staggers. Just think for example what might lie below the surfaces of celestial bodies all across the far flung reaches of our universe. What we feel, even as we learn, is an ever-renewed sense of wonder, indeed, a powerful sense of awe – and of Divine inspiration"(Aga Khan IV, Delegation of the Ismaili Imamat, Ottawa, Canada, December 6th 2008)

"In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

"....AND SHOULD'NT IB SCIENCE STUDENTS not learn about Ibn al-Haytham, the Muslim scholar who developed modern optics, as well as his predecessors Euclid and Ptolemy, whose ideas he challenged.....The legacy which I am describing actually goes back more than a thousand years, to the time when our forefathers, the Fatimid Imam-Caliphs of Egypt, founded Al-Azhar University and the Academy of Knowledge in Cairo. For many centuries, a commitment to learning was a central element in far-flung Islamic cultures. That commitment has continued in my own Imamat through the founding of the Aga Khan University and the University of Central Asia and through the recent establishment of a new Aga Khan Academies Program."(Aga Khan IV, "The Peterson Lecture" on the International Baccalaureate, Atlanta, Georgia, USA, 18 April 2008)

"The second great historical lesson to be learnt is that the Muslim world has always been wide open to every aspect of human existence. The sciences, society, art, the oceans, the environment and the cosmos have all contributed to the great moments in the history of Muslim civilisations. The Qur’an itself repeatedly recommends Muslims to become better educated in order better to understand God’s creation"(Closing Address by His Highness Aga Khan IV at the "Musée-Musées" Round Table Louvre Museum, Paris, France, October 17th 2007)

"......The Quran tells us that signs of Allah’s Sovereignty are found in the contemplation of His Creation - in the heavens and the earth, the night and the day, the clouds and the seas, the winds and the waters...."(Aga Khan IV, Kampala, Uganda, August 22 2007)

"Of the Abrahamic faiths, Islam is probably the one that places the greatest emphasis on knowledge. The purpose is to understand God's creation, and therefore it is a faith which is eminently logical. Islam is a faith of reason"(Aga Khan IV, Spiegel Magazine interview, Germany, Oct 9th 2006)

"Astronomy, the so-called “Science of the Universe” was a field of particular distinction in Islamic civilization-–in sharp contrast to the weakness of Islamic countries in the field of Space research today. In this field, as in others, intellectual leadership is never a static condition, but something which is always shifting and always dynamic"(Aga Khan IV, Convocation, American University of Cairo, Cairo, Egypt, June 15th 2006)

"In this context, would it not also be relevant to consider how, above all, it has been the Qur'anic notion of the universe as an expression of Allah's will and creation that has inspired, in diverse Muslim communities, generations of artists, scientists and philosophers? Scientific pursuits, philosophic inquiry and artistic endeavour are all seen as the response of the faithful to the recurring call of the Qur'an to ponder the creation as a way to understand Allah's benevolent majesty. As Sura al-Baqara proclaims: 'Wherever you turn, there is the face of Allah'.The famous verse of 'light' in the Qur'an, the Ayat al-Nur, whose first line is rendered here in the mural behind me, inspires among Muslims a reflection on the sacred, the transcendent. It hints at a cosmos full of signs and symbols that evoke the perfection of Allah's creation and mercy"(Aga Khan IV,Speech, Institute of Ismaili Studies, October 2003, London, U.K.)

"From the seventh century to the thirteenth century, the Muslim civilizations dominated world culture, accepting, adopting, using and preserving all preceding study of mathematics, philosophy, medicine and astronomy, among other areas of learning. The Islamic field of thought and knowledge included and added to much of the information on which all civilisations are founded. And yet this fact is seldom acknowledged today, be it in the West or in the Muslim world, and this amnesia has left a six hundred year gap in the history of human thought"(Aga Khan IV, Brown University, Providence, Rhode Island, USA, 1996)

"An institution dedicated to proceeding beyond known limits must be committed to independent thinking. In a university scholars engage both orthodox and unorthodox ideas, seeking truth and understanding wherever they may be found. That process is often facilitated by an independent governance structure, which serves to ensure that the university adheres to its fundamental mission and is not pressured to compromise its work for short-term advantage. For a Muslim university it is appropriate to see learning and knowledge as a continuing acknowledgement of Allah's magnificence"(Aga Khan IV, Speech, 1993, Aga Khan University, Karachi, Pakistan)

"Science is a wonderful, powerful tool and research budgets are essential. But Science is only the beginning in the new age we are entering. Islam does not perceive the world as two seperate domains of mind and spirit, science and belief. Science and the search for knowledge are an expression of man's designated role in the universe, but they do not define that role totally....."(Aga Khan IV, McMaster University Convocation, Hamilton, Ontario, Canada, May 15th 1987)

"The Divine Intellect, Aql-i Kull, both transcends and informs the human intellect. It is this Intellect which enables man to strive towards two aims dictated by the faith: that he should reflect upon the environment Allah has given him and that he should know himself. It is the Light of the Intellect which distinguishes the complete human being from the human animal, and developing that intellect requires free inquiry. The man of faith, who fails to pursue intellectual search is likely to have only a limited comprehension of Allah's creation. Indeed, it is man's intellect that enables him to expand his vision of that creation"(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11, 1985)

"The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims. Exchanges of knowledge between institutions and nations and the widening of man's intellectual horizons are essentially Islamic concepts. The Faith urges freedom of intellectual enquiry and this freedom does not mean that knowledge will lose its spiritual dimension. That dimension is indeed itself a field for intellectual enquiry. I can not illustrate this interdependence of spiritual inspiration and learning better than by recounting a dialogue between Ibn Sina, the philosopher, and Abu Said Abu -Khyar, the Sufi mystic. Ibn Sina remarked, "Whatever I know, he sees". To which Abu Said replied," Whatever I see, he knows"."(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11th 1985)

“Muslims believe in an all-encompassing unit of man and nature. To them there is no fundamental division between the spiritual and the material while the whole world, whether it be the earth, sea or air, or the living creatures that inhabit them, is an expression of God’s creation.”(Aga Khan IV, University of Virginia, Charlottesville, Virginia, USA, 13 April 1984)

"One of the first and greatest research centres, the Bayt al-Hikmah established in Baghdad in 830, led Islam in translating philosophical and scientific works from Greek, Roman, Persian and Indian classics. By the art of translation, learning was assimilated from other civilizations"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"Indeed, one strength of Islam has always lain in its belief that creation is not static but continuous, that through scientific and other endeavours, God has opened and continues to open new windows for us to see the marvels of His creation"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"Our religious leadership must be acutely aware of secular trends, including those generated by this age of science and technology. Equally, our academic or secular elite must be deeply aware of Muslim history, of the scale and depth of leadership exercised by the Islamic empire of the past in all fields"(Aga Khan IV, 6th February 1970, Hyderabad, Pakistan)

"God has given us the miracle of life with all its attributes: the extraordinary manifestations of sunrise and sunset, of sickness and recovery, of birth and death, but surely if He has given us the means with which to remove ourselves from this world so as to go to other parts of the Universe, we can but accept as further manifestations the creation and destructions of stars, the birth and death of atomic particles, the flighting new sound and light waves. I am afraid that the torch of intellectual discovery, the attraction of the unknown, the desire for intellectual self-perfection have left us"(Aga Khan IV,Speech, 1963, Mindanao, Phillipines)

"The creation according to Islam is not a unique act in a given time but a perpetual and constant event; and God supports and sustains all existence at every moment by His will and His thought. Outside His will, outside His thought, all is nothing, even the things which seem to us absolutely self-evident such as space and time. Allah alone wishes: the Universe exists; and all manifestations are as a witness of the Divine Will"(Memoirs of Aga Khan III, 1954)

"Thus Islam's basic principle can only be defined as mono-realism and not as monotheism. Consider, for example, the opening declaration of every Islamic prayer: "Allah-o-Akbar". What does that mean? There can be no doubt that the second word of the declaration likens the character of Allah to a matrix which contains all and gives existence to the infinite, to space, to time, to the Universe, to all active and passive forces imaginable, to life and to the soul. Imam Hassan has explained the Islamic doctrine of God and the Universe by analogy with the sun and its reflection in the pool of a fountain; there is certainly a reflection or image of the sun, but with what poverty and with what little reality; how small and pale is the likeness between this impalpable image and the immense, blazing, white-hot glory of the celestial sphere itself. Allah is the sun; and the Universe, as we know it in all its magnitude, and time, with its power, are nothing more than the reflection of the Absolute in the mirror of the fountain"(Memoirs of Aga Khan III, 1954)

"Islam is fundamentally in its very nature a natural religion. Throughout the Quran God's signs (Ayats) are referred to as the natural phenomenon, the law and order of the universe, the exactitudes and consequences of the relations between natural phenomenon in cause and effect. Over and over, the stars, sun, moon, earthquakes, fruits of the earth and trees are mentioned as the signs of divine power, divine law and divine order. Even in the Ayeh of Noor, divine is referred to as the natural phenomenon of light and even references are made to the fruit of the earth. During the great period of Islam, Muslims did not forget these principles of their religion"(Aga Khan III, April 4th 1952)

Chapter 21, Verse 30: Do not the unbelievers see that the heavens and the earth were joined together before We clove them asunder, and of water fashioned every thing? Will they not then believe?(Noble Quran, 7th Century CE)

Chapter 51, verse 47: We built the heavens with might, and We expand it wide(Noble Quran, 7th Century CE)

Chapter79, verse 30: And then he gave the earth an oval form(Noble Quran, 7th Century CE)

Chapter 86, verse 11: I swear by the reciprocating heaven.....(Noble Quran, 7th Century CE)

"Seek knowledge from the cradle to the grave"(Prophet Muhammad, circa 632CE)"

"Seek knowledge, even in China"(Prophet Muhammad, circa 632CE)

"One hour of contemplation on the works of the Creator is better than a thousand hours of prayer"(Prophet Muhammad, circa 632CE)

"The ink of the scholar is better than the blood of the martyr"(Prophet Muhammad, circa 632CE)

"All human beings, by their nature, desire to know."(Aristotle, The Metaphysics, circa 322BC)

The above are 30 quotes and excerpts taken from Blogpost Four Hundred, a collection of around 100 quotes on the subjects of Knowledge, Intellect, Creation, Science and Religion:
http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html



Easy Nash

The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)

496)Worried About H1N1 Flu This Fall?First Learn About Your Immune System+Viruses:What Are They Made Of+How Do They Operate?Marvels Of God's Creation.

This blogpost contains two seperate articles in sequence:
A)How Your Immune System Works
B)How Viruses Work


A)HOW YOUR IMMUNE SYSTEM WORKS
by Marshall Brain

Browse the article How Your Immune System Works


Introduction to How Your Immune System Works


Inside your body there is a mechanism designed to defend you from millions of bacteria, microbes, viruses, toxins and parasites.

Inside your body there is an amazing protectio­n mechanism called the immune system. It is designed to defend you against millions of bacteria, microbes, viruses, toxins and parasites that would love to invade your body. To understand the power of the immune system, all that you have to do is look at what happens to anything once it dies. That sounds gross, but it does show you something very important about your immune system.

When something dies, its immune system (along with everything else) shuts down. In a matter of hours, the body is invaded by all sorts of bacteria, microbes, parasites... None of these things are able to get in when your immune system is working, but the moment your immune system stops the door is wide open. Once you die it only takes a few weeks for these organisms to completely dismantle your body and carry it away, until all that's left is a skeleton. Obviously your immune system is doing something amazing to keep all of that dismantling from happening when you are alive.

The immune system is complex, intricate and interesting. And there are at least two good reasons for you to know more about it. First, it is just plain fascinating to understand where things like fevers, hives, inflammation, etc., come from when they happen inside your own body. You also hear a lot about the immune system in the news as new parts of it are understood and new drugs come on the market -- knowing about the immune system makes these news stories understandable. In this article, we will take a look at how your immune system works so that you can understand what it is doing for you each day, as well as what it is not.


Seeing Your Immune System

Your immune system works around the clock in thousands of different ways, but it does its work largely unnoticed. One thing that causes us to really notice our immune system is when it fails for some reason. We also notice it when it does something that has a side effect we can see or feel. Here are several examples:

1)When you get a cut, all sorts of bacteria and viruses enter your body through the break in the skin. When you get a splinter you also have the sliver of wood as a foreign object inside your body. Your immune system responds and eliminates the invaders while the skin heals itself and seals the puncture. In rare cases the immune system misses something and the cut gets infected. It gets inflamed and will often fill with pus. Inflammation and pus are both side-effects of the immune system doing its job.

2)When a mosquito bites you, you get a red, itchy bump. That too is a visible sign of your immune system at work.

3)Each day you inhale thousands of germs (bacteria and viruses) that are floating in the air. Your immune system deals with all of them without a problem. Occasionally a germ gets past the immune system and you catch a cold, get the flu or worse. A cold or flu is a visible sign that your immune system failed to stop the germ. The fact that you get over the cold or flu is a visible sign that your immune system was able to eliminate the invader after learning about it. If your immune system did nothing, you would never get over a cold or anything else.

4)Each day you also eat hundreds of germs, and again most of these die in the saliva or the acid of the stomach. Occasionally, however, one gets through and causes food poisoning. There is normally a very visible effect of this breach of the immune system: vomiting and diarrhea are two of the most common symptoms.

5)There are also all kinds of human ailments that are caused by the immune system working in unexpected or incorrect ways that cause problems. For example, some people have allergies. Allergies are really just the immune system overreacting to certain stimuli that other people don't react to at all. Some people have diabetes, which is caused by the immune system inappropriately attacking cells in the pancreas and destroying them. Some people have rheumatoid arthritis, which is caused by the immune system acting inappropriately in the joints. In many different diseases, the cause is actually an immune system error.

6)Finally, we sometimes see the immune system because it prevents us from doing things that would be otherwise beneficial. For example, organ transplants are much harder than they should be because the immune system often rejects the transplanted organ.


Basics of the Immune System

Let's start at the beginning. What does it mean when someone says "I feel sick today?" What is a disease? By understanding the different kinds of diseases it is possible to see what types of disease the immune system helps you handle.

When you "get sick", your body is not able to work properly or at its full potential. There are many different ways for you to get sick -- here are some of them:

1)Mechanical damage - If you break a bone or tear a ligament you will be "sick" (your body will not be able to perform at its full potential). The cause of the problem is something that is easy to understand and visible.

2)Vitamin or mineral deficiency - If you do not get enough vitamin D your body is not able to metabolize calcium properly and you get a disease known as rickets. People with rickets have weak bones (they break easily) and deformities because the bones do not grow properly. If you do not get enough vitamin C you get scurvy, which causes swollen and bleeding gums, swollen joints and bruising. If you do not get enough iron you get anemia, and so on.

3)Organ degradation - In some cases an organ is damaged or weakened. For example, one form of "heart disease" is caused by obstructions in the blood vessels leading to the heart muscle, so that the heart does not get enough blood. One form of "liver disease", known as Cirrhosis, is caused by damage to liver cells (drinking too much alcohol is one cause).

4)Genetic disease - A genetic disease is caused by a coding error in the DNA. The coding error causes too much or too little of certain proteins to be made, and that causes problems at the cellular level. For example, albinism is caused by a lack of an enzyme called tyrosinase. That missing enzyme means that the body cannot manufacture melanin, the natural pigment that causes hair color, eye color and tanning. Because of the lack of melanin, people with this genetic problem are extremely sensitive to the UV rays in sunlight.

5)Cancer - Occasionally a cell will change in a way that causes it to reproduce uncontrollably. For example, when cells in the skin called melanocytes are damaged by ultraviolet radiation in sunlight they change in a characteristic way into a cancerous form of cell. The visible cancer that appears as a tumor on the skin is called melanoma. (See How Sun Tans and Sunburns Work for more information.)


Viral or Bacterial Infection

When a virus or bacteria (also known generically as a germ) invades your body and reproduces, it normally causes problems. Generally the germ's presence produces some side effect that makes you sick. For example, the strep throat bacteria (Streptococcus) releases a toxin that causes inflammation in your throat. The polio virus releases toxins that destroy nerve cells (often leading to paralysis). Some bacteria are benign or beneficial (for example, we all have millions of bacteria in our intestines and they help digest food), but many are harmful once they get into the body or the bloodstream.

Viral and bacterial infections are by far the most common causes of illness for most people. They cause things like colds, influenza, measles, mumps, malaria, AIDS and so on.

The job of your immune system is to protect your body from these infections. The immune system protects you in three different ways:

1)It creates a barrier that prevents bacteria and viruses from entering your body.

2)If a bacteria or virus does get into the body, the immune system tries to detect and eliminate it before it can make itself at home and reproduce.

3)If the virus or bacteria is able to reproduce and start causing problems, your immune system is in charge of eliminating it.

The immune system also has several other important jobs. For example, your immune system can detect cancer in early stages and eliminate it in many cases.

Bacteria and Viruses
Your body is a multi-cellular organism made up of perhaps 100 trillion cells. The cells in your body are fairly complicated machines. Each one has a nucleus, energy production equipment, etc. Bacteria are single-celled organisms that are much simpler. For example, they have no nucleus. They are perhaps 1/100th the size of a human cell and might measure 1 micrometer long. Bacteria are completely independent organisms able to eat and reproduce - they are sort of like fish swimming in the ocean of your body. Under the right conditions bacteria reproduce very quickly: One bacteria divides into two separate bacteria perhaps once every 20 or 30 minutes. At that rate, one bacteria can become millions in just a few hours.

A virus is a different breed altogether. A virus is not really alive. A virus particle is nothing but a fragment of DNA in a protective coat. The virus comes in contact with a cell, attaches itself to the cell wall and injects its DNA (and perhaps a few enzymes) into the cell. The DNA uses the machinery inside the living cell to reproduce new virus particles. Eventually the hijacked cell dies and bursts, freeing the new virus particles; or the viral particles may bud off of the cell so it remains alive. In either case, the cell is a factory for the virus.


Components of the Immune System

One of the funny things about the immune system is that it has been working inside your body your entire life but you probably know almost nothing about it. For example, you are probably aware that inside your chest you have an organ called a "heart". Who doesn't know that they have a heart? You have probably also heard about the fact that you have lungs and a liver and kidneys. But have you even heard about your thymus? There's a good chance you don't even know that you have a thymus, yet its there in your chest right next to your heart. There are many other parts of the immune system that are just as obscure, so let's start by learning about all of the parts.

The most obvious part of the immune system is what you can see. For example, skin is an important part of the immune system. It acts as a primary boundary between germs and your body. Part of your skin's job is to act as a barrier in much the same way we use plastic wrap to protect food. Skin is tough and generally impermeable to bacteria and viruses. The epidermis contains special cells called Langerhans cells (mixed in with the melanocytes in the basal layer) that are an important early-warning component in the immune system. The skin also secretes antibacterial substances. These substances explain why you don't wake up in the morning with a layer of mold growing on your skin -- most bacteria and spores that land on the skin die quickly.

Your nose, mouth and eyes are also obvious entry points for germs. Tears and mucus contain an enzyme (lysozyme) that breaks down the cell wall of many bacteria. Saliva is also anti-bacterial. Since the nasal passage and lungs are coated in mucus, many germs not killed immediately are trapped in the mucus and soon swallowed. Mast cells also line the nasal passages, throat, lungs and skin. Any bacteria or virus that wants to gain entry to your body must first make it past these defenses.

Once inside the body, a germ deals with the immune system at a different level. The major components of the immune system are:

Thymus
Spleen
Lymph system
Bone marrow
White blood cells
Antibodies
Complement system

Hormones Let's look at each of these components in detail.


Lymph System

The lymph system is most familiar to people because doctors and mothers often check for "swollen lymph nodes" in the neck. It turns out that the lymph nodes are just one part of a system that extends throughout your body in much the same way your blood vessels do. The main difference between the blood flowing in the circulatory system and the lymph flowing in the lymph system is that blood is pressurized by the heart, while the lymph system is passive. There is no "lymph pump" like there is a "blood pump" (the heart). Instead, fluids ooze into the lymph system and get pushed by normal body and muscle motion to the lymph nodes. This is very much like the water and sewer systems in a community. Water is actively pressurized, while sewage is passive and flows by gravity.

Lymph is a clearish liquid that bathes the cells with water and nutrients. Lymph is blood plasma -- the liquid that makes up blood minus the red and white cells. Think about it -- each cell does not have its own private blood vessel feeding it, yet it has to get food, water, and oxygen to survive. Blood transfers these materials to the lymph through the capillary walls, and lymph carries it to the cells. The cells also produce proteins and waste products and the lymph absorbs these products and carries them away. Any random bacteria that enter the body also find their way into this inter-cell fluid. One job of the lymph system is to drain and filter these fluids to detect and remove the bacteria. Small lymph vessels collect the liquid and move it toward larger vessels so that the fluid finally arrives at the lymph nodes for processing.

Click play to see how the lymph nodes work.If the animation above isn't working, click here to get the Shockwave player.

Lymph nodes contain filtering tissue and a large number of lymph cells. When fighting certain bacterial infections, the lymph nodes swell with bacteria and the cells fighting the bacteria, to the point where you can actually feel them. Swollen lymph nodes are therefore a good indication that you have an infection of some sort.

Once lymph has been filtered through the lymph nodes it re-enters the bloodstream.


Thymus

The thymus lives in your chest, between your breast bone and your heart. It is responsible for producing T-cells (see the next section), and is especially important in newborn babies - without a thymus a baby's immune system collapses and the baby will die. The thymus seems to be much less important in adults - for example, you can remove it and an adult will live because other parts of the immune system can handle the load. However, the thymus is important, especially to T cell maturation (as we will see in the section on white blood cells below).


Spleen

The spleen filters the blood looking for foreign cells (the spleen is also looking for old red blood cells in need of replacement). A person missing their spleen gets sick much more often than someone with a spleen.


Bone marrow

Bone marrow produces new blood cells, both red and white. In the case of red blood cells the cells are fully formed in the marrow and then enter the bloodstream. In the case of some white blood cells, the cells mature elsewhere. The marrow produces all blood cells from stem cells. They are called "stem cells" because they can branch off and become many different types of cells - they are precursors to different cell types. Stem cells change into actual, specific types of white blood cells.


White blood cells

White blood cells are described in detail in the next section.


Antibodies

Antibodies (also referred to as immunoglobulins and gammaglobulins) are produced by white blood cells. They are Y-shaped proteins that each respond to a specific antigen (bacteria, virus or toxin). Each antibody has a special section (at the tips of the two branches of the Y) that is sensitive to a specific antigen and binds to it in some way. When an antibody binds to a toxin it is called an antitoxin (if the toxin comes from some form of venom, it is called an antivenin). The binding generally disables the chemical action of the toxin. When an antibody binds to the outer coat of a virus particle or the cell wall of a bacterium it can stop their movement through cell walls. Or a large number of antibodies can bind to an invader and signal to the complement system that the invader needs to be removed.

Antibodies come in five classes:

Immunoglobulin A (IgA)
Immunoglobulin D (IgD)
Immunoglobulin E (IgE)
Immunoglobulin G (IgG)
Immunoglobulin M (IgM)

Whenever you see an abbreviation like IgE in a medical document, you now know that what they are talking about is an antibody.

For additional information on antibodies see The Antibody Resource Page.


Complement System

The complement system, like antibodies, is a series of proteins. There are millions of different antibodies in your blood stream, each sensitive to a specific antigen. There are only a handful of proteins in the complement system, and they are floating freely in your blood. Complements are manufactured in the liver. The complement proteins are activated by and work with (complement) the antibodies, hence the name. They cause lysing (bursting) of cells and signal to phagocytes that a cell needs to be removed.

For additional information on complements, see The Complement System.


Hormones

There are several hormones generated by components of the immune system. These hormones are known generally as lymphokines. It is also known that certain hormones in the body suppress the immune system. Steroids and corticosteroids (components of adrenaline) suppress the immune system.

Tymosin (thought to be produced by the thymus) is a hormone that encourages lymphocyte production (a lymphocyte is a form of white blood cell - see below). Interleukins are another type of hormone generated by white blood cells. For example, Interleukin-1 is produced by macrophages after they eat a foreign cell. IL-1 has an interesting side-effect - when it reaches the hypothalamus it produces fever and fatigue. The raised temperature of a fever is known to kill some bacteria.

For additional information see Manifestations of Infection: Fever and IL-1.


Tumor Necrosis Factor

Tumor Necrosis Factor (TNF) is also produced by macrophages. It is able to kill tumor cells, and it also promotes the creation of new blood vessels so it is important to healing.


Interferon

Interferon interferes with viruses (hence the name) and is produced by most cells in the body. Interferons, like antibodies and complements, are proteins, and their job is to let cells signal to one another. When a cell detects interferon from other cells, it produces proteins that help prevent viral replication in the cell.


White Blood Cells

You are probably aware of the fact that you have "red blood cells" and "white blood cells" in your blood. The white blood cells are probably the most important part of your immune system. And it turns out that "white blood cells" are actually a whole collection of different cells that work together to destroy bacteria and viruses. Here are all of the different types, names and classifications of white blood cells working inside your body right now:

Leukocytes
Lymphocyte
Monocytes
Granulocytes
B-cells
Plasma cells
T-cells
Helper T-cells
Killer T-cells
Suppressor T-cells
Natural killer cells
Neutrophils
Eosinophils
Basophils
Phagocytes
Macrophages


Leukocytes

Learning all of these different names and the function of each cell type takes a bit of effort, but you can understand scientific articles a lot better once you get it all figured out! Here's a quick summary to help you get all of the different cell types organized in your brain.

All white blood cells are known officially as leukocytes. White blood cells are not like normal cells in the body -- they actually act like independent, living single-cell organisms able to move and capture things on their own. White blood cells behave very much like amoeba in their movements and are able to engulf other cells and bacteria. Many white blood cells cannot divide and reproduce on their own, but instead have a factory somewhere in the body that produces them. That factory is the bone marrow.

Leukocytes are divided into three classes:

1)Granulocytes - Granulocytes make up 50% to 60% of all leukocytes. Granulocytes are themselves divided into three classes: neutrophils, eosinophils and basophils. Granulocytes get their name because they contain granules, and these granules contain different chemicals depending on the type of cell.

2)Lymphocyte - Lymphocytes make up 30% to 40% of all leukocytes. Lymphocytes come in two classes: B cells (those that mature in bone marrow) and T cells (those that mature in the thymus).

3)Monocyte - Monocytes make up 7% or so of all leukocytes. Monocytes evolve into macrophages.

All white blood cells start in bone marrow as stem cells. Stem cells are generic cells that can form into the many different types of leukocytes as they mature. For example, you can take a mouse, irradiate it to kill off its bone marrow's ability to produce new blood cells, and then inject stem cells into the mouse's blood stream. The stem cells will divide and differentiate into all different types of white blood cells. A "bone marrow transplant" is accomplished simply by injecting stem cells from a donor into the blood stream. The stem cells find their way, almost magically, into the marrow and make their home there.


Different Roles

Each of the different types of white blood cells have a special role in the immune system, and many are able to transform themselves in different ways. The following descriptions help to understand the roles of the different cells.

Neutrophils are by far the most common form of white blood cells that you have in your body. Your bone marrow produces trillions of them every day and releases them into the bloodstream, but their life span is short -- generally less than a day. Once in the bloodstream neutrophils can move through capillary walls into tissue. Neutorphils are attracted to foreign material, inflammation and bacteria. If you get a splinter or a cut, neutrophils will be attracted by a process called chemotaxis. Many single-celled organisms use this same process -- chemotaxis lets motile cells move toward higher concentrations of a chemical. Once a neutrophil finds a foreign particle or a bacteria it will engulf it, releasing enzymes, hydrogen peroxide and other chemicals from its granules to kill the bacteria. In a site of serious infection (where lots of bacteria have reproduced in the area), pus will form. Pus is simply dead neutrophils and other cellular debris.

Eosinophils and basophils are far less common than neutrophils. Eosinophils seem focused on parasites in the skin and the lungs, while Basophils carry histamine and therefore important (along with mast cells) to causing inflammation. From the immune system's standpoint inflammation is a good thing. It brings in more blood and it dilates capillary walls so that more immune system cells can get to the site of infection.

Of all blood cells, macrophages are the biggest (hence the name "macro"). Monocytes are released by the bone marrow, float in the bloodstream, enter tissue and turn into macrophages. Most boundary tissue has its own devoted macrophages. For example, alveolar macrophages live in the lungs and keep the lungs clean (by ingesting foreign particles like smoke and dust) and disease free (by ingesting bacteria and microbes). Macrophages are called langerhans cells when they live in the skin. Macrophages also swim freely. One of their jobs is to clean up dead neutrophils -- macropghages clean up pus, for example, as part of the healing process.

Click the play button to see some of the specialized white blood cells in action.If the animation above isn't working, click here to get the Shock wave player.

The lymphocytes handle most of the bacterial and viral infections that we get. Lymphocytes start in the bone marrow. Those destined to become B cells develop in the marrow before entering the bloodstream. T cells start in the marrow but migrate through the bloodstream to the thymus and mature there. T cells and B cells are often found in the bloodstream but tend to concentrate in lymph tissue such as the lymph nodes, the thymus and the spleen. There is also quite a bit of lymph tissue in the digestive system. B cells and T cells have different functions.
B cells, when stimulated, mature into plasma cells -- these are the cells that produce antibodies. A specific B cell is tuned to a specific germ, and when the germ is present in the body the B cell clones itself and produces millions of antibodies designed to eliminate the germ.

T cells, on the other hand, actually bump up against cells and kill them. T cells known as Killer T cells can detect cells in your body that are harboring viruses, and when it detects such a cell it kills it. Two other types of T cells, known as Helper and Suppressor T cells, help sensitize killer T cells and control the immune response.


T Cells

Helper T cells are actually quite important and interesting. They are activated by Interleukin-1, produced by macrophages. Once activated, Helper T cells produce Interleukin-2, then interferon and other chemicals. These chemicals activate B cells so that they produce antibodies. The complexity and level of interaction between neutrophils, macrophages, T cells and B cells is really quite amazing.

Because white blood cells are so important to the immune system, they are used as a measure of immune system health. When you hear that someone has a "strong immune system" or a "suppressed immune system", one way it was determined was by counting different types of white blood cells in a blood sample. A normal white blood cell count is in the range of 4,000 to 11,000 cells per microliter of blood. 1.8 to 2.0 helper T-cells per suppressor T-cell is normal. A normal absolute neutrophil count (ANC) is in the range of 1,500 to 8,000 cells per microliter. An article like Introduction to Hematology can help you learn more about white blood cells in general and the different types of white blood cells found in your body.

One important question to ask about white blood cells (and several other parts of the immune system) is, "How does a white blood cell know what to attack and what to leave alone? Why doesn't a white blood cell attack every cell in the body?" There is a system built into all of the cells in your body called the Major Histocompatibility Complex (MHC) (also known as the Human Leukocyte Antigen (HLA)) that marks the cells in your body as "you". Anything that the immune system finds that does not have these markings (or that has the wrong markings) is definitely "not you" and is therefore fair game. Encyclopedia Britannica has this to say about the MHC:

"There are two major types of MHC protein molecules--class I and class II--that span the membrane of almost every cell in an organism. In humans these molecules are encoded by several genes all clustered in the same region on chromosome 6. Each gene has an unusual number of alleles (alternate forms of a gene). As a result, it is very rare for two individuals to have the same set of MHC molecules, which are collectively called a tissue type.

MHC molecules are important components of the immune response. They allow cells that have been invaded by an infectious organism to be detected by cells of the immune system called T lymphocytes, or T cells. The MHC molecules do this by presenting fragments of proteins (peptides) belonging to the invader on the surface of the cell. The T cell recognizes the foreign peptide attached to the MHC molecule and binds to it, an action that stimulates the T cell to either destroy or cure the infected cell. In uninfected healthy cells the MHC molecule presents peptides from its own cell (self peptides), to which T cells do not normally react. However, if the immune mechanism malfunctions and T cells react against self peptides, an autoimmune disease arises."

See Biology of the Immune System and Major Histocompatibility Complex for additional details.


Vaccinations

There are many diseases that, if you catch them once, you will never catch again. Measles is a good example, as is chicken pox. What happens with these diseases is that they make it into your body and start reproducing. The immune system gears up to eliminate them. In your body you already have B cells that can recognize the virus and produce antibodies for it. However, there are only a few of these cells for each antibody. Once a particlular disease is recognized by these few specific B cells, the B cells turn into plasma cells, clone themselves and start pumping out antibodies. This process takes time, but the disease runs it course and is eventually eliminated. However, while it is being eliminated, other B cells for the disease clone themselves but do not generate antibodies. This second set of B cells remains in your body for years, so if the disease reappears your body is able to eliminate it immediately before it can do anything to you.

A vaccine is a weakened form of a disease. It is either a killed form of the disease, or it is a similar but less virulent strain. Once inside your body your immune system mounts the same defense, but because the disease is different or weaker you get few or no symptoms of the disease. Now, when the real disease invades your body, your body is able to eliminate it immediately.

Vaccines exist for all sorts of diseases, both viral and bacterial: measles, mumps, whooping cough, tuberculosis, smallpox, polio, typhoid, etc.

Many diseases cannot be cured by vaccines, however. The common cold and Influenza are two good examples. These diseases either mutate so quickly or have so many different strains in the wild that it is impossible to inject all of them into your body. Each time you get the flu, for example, you are getting a different strain of the same disease.


AIDS

AIDS (Acquired Immune Deficiency Syndrome) is a disease caused by HIV (the Human Immunodeficiency Virus). This is a particularly problematic disease for the immune system because the virus actually attacks immune system cells. In particular, it reproduces inside Helper T cells and kills them in the process. Without Helper T cells to orchestrate things, the immune system eventually collapses and the victim dies of some other infection that the immune system would normally be able to handle. See How AIDS Works as well as the links below for more information.

HIV Lifecycle
AIDS Research
AIDS and HIV Drugs
AIDS/HIV Research and Treatment


How Antibiotics Work

Sometimes your immune system is not able to activate itself quickly enough to outpace the reproductive rate of a certain bacteria, or the bacteria is producing a toxin so quickly that it will cause permanent damage before the immune system can eliminate the bacteria. In these cases it would be nice to help the immune system by killing the offending bacteria directly.

Antibiotics work on bacterial infections. Antibiotics are chemicals that kill the bacteria cells but do not affect the cells that make up your body. For example, many antibiotics interrupt the machinery inside bacterial cells that builds the cell wall. Human cells do not contain this machinery, so they are unaffected. Different antibiotics work on different parts of bacterial machinery, so each one is more or less effective on specific types of bacteria. You can see that, because a virus is not alive, antibiotics have no effect on a virus.

One problem with antibiotics is that they lose effectiveness over time. If you take an antibiotic it will normally kill all of the bacteria it targets over the course of a week or 10 days. You will feel better very quickly (in just a day or two) because the antibiotic kills the majority of the targeted bacteria very quickly. However, on occasion one of the bacterial offspring will contain a mutation that is able to survive the specific antibiotic. This bacteria will then reproduce and the whole disease mutates. Eventually the new strain is infecting everyone and the old antibiotic has no effect on it. This process has become more and more of a problem over time and has become a significant concern in the medical community.


Immune System Mistakes

Sometimes the immune system makes a mistake. One type of mistake is called autoimmunity: the immune system for some reason attacks your own body in the same way it would normally attack a germ. Two common diseases are caused by immune system mistakes. Juvenile-onset diabetes is caused by the immune system attacking and eliminating the cells in the pancreas that produce insulin. Rheumatoid arthritis is caused by the immune system attacking tissues inside the joints.

Allergies are another form of immune system error. For some reason, in people with allergies, the immune system strongly reacts to an allergen that should be ignored. The allergen might be a certain food, or a certain type of pollen, or a certain type of animal fur. For example, a person allergic to a certain pollen will get a runny nose, watery eyes, sneezing, etc. This reaction is caused primarily by mast cells in the nasal passages. In reaction to the pollen the mast cells release histamine. Histamine has the effect of causing inflammation, which allows fluid to flow from blood vessels. Histamine also causes itching. To eliminate these symptoms the drug of choice is, of course, an antihistamine.

The last example of an immune system mistake is the effect the immune system has on transplanted tissue. This really isn't a mistake, but it makes organ and tissue transplants nearly impossible. When the foreign tissue is placed inside your body, its cells do not contain the correct identification. Your immune system therefore attacks the tissue. The problem cannot be prevented, but can be diminished by carefully matching the tissue donor with the recipient and by using immunosuppressing drugs to try to prevent an immune system reaction. Of course, by suppressing the immune system these drugs open the patient to opportunistic infections.

http://health.howstuffworks.com/immune-system.htm/printable




B)HOW VIRUSES WORK
by Craig Freudenrich, Ph.D.

Browse the article How Viruses Work


Introduction to How Viruses Work

Most of us at one time or another have had colds or the flu, and we are especially vulnerable during the cold and flu season. The symptoms -- fever, congestion, coughing, sore throat -- spread through offices, schools and homes, no matter where in the world we live. Colds and flu (influenza) are caused by viruses. Viruses are responsible for many other serious, often deadly, diseases including acquired immunodeficiency syndrome (AIDS), Ebola hemorrhagic fever, infectious hepatitis and herpes. How can viruses cause so much trouble? What makes us so vulnerable to them, and what makes them spread?

Learn More
How the Flu Works
How can light kill viruses?
Discovery.com: Swine Flu News

In this article, we will explore the world of viruses. We'll talk about what a virus is, what viruses look like, how they infect us and how we can reduce the risk of infection. And you'll learn why you feel so miserable when a cold virus attacks your body!


What is a Virus?

If you have read How Cells Work, you know how both bacteria cells and the cells in your body work. A cell is a stand-alone living entity able to eat, grow and reproduce. Viruses are nothing like that. If you could look at a virus, you would see that a virus is a tiny particle. Virus particles are about one-millionth of an inch (17 to 300 nanometers) long. Viruses are about a thousand times smaller than bacteria, and bacteria are much smaller than most human cells. Viruses are so small that most cannot be seen with a light microscope, but must be observed with an electron microscope.


A virus particle, or virion, consists of the following:

1)Nucleic acid - Set of genetic instructions, either DNA or RNA, either single-stranded or double-stranded (see How Cells Work for details on DNA and RNA)
2)Coat of protein - Surrounds the DNA or RNA to protect it
3)Lipid membrane - Surrounds the protein coat (found only in some viruses, including influenza; these types of viruses are called enveloped viruses as opposed to naked viruses)

Viruses vary widely in their shape and complexity. Some look like round popcorn balls, while others have a complicated shape that looks like a spider or the Apollo lunar lander.

Unlike human cells or bacteria, viruses do not contain the chemical machinery (enzymes) needed to carry out the chemical reactions for life. Instead, viruses carry only one or two enzymes that decode their genetic instructions. So, a virus must have a host cell (bacteria, plant or animal) in which to live and make more viruses. Outside of a host cell, viruses cannot function. For this reason, viruses tread the fine line that separates living things from nonliving things. Most scientists agree that viruses are alive because of what happens when they infect a host cell.


How a Virus Infects You

Viruses lie around our environment all of the time just waiting for a host cell to come along. They can enter us through the nose, mouth or breaks in the skin (see How the Immune System Works for details). Once inside, they find a host cell to infect. For example, cold and flu viruses will attack cells that line the respiratory or digestive tracts. The human immunodeficiency virus (HIV), which causes AIDS, attacks the T-cells of the immune system.

In the lytic cycle, the virus reproduces itself using the host cell's chemical machinery. The red spiral lines in the drawing indicate the virus's genetic material. The orange portion is the outer shell that protects it.

Regardless of the type of host cell, all viruses follow the same basic steps in what is known as the lytic cycle (see figure in article):

1)A virus particle attaches to a host cell.
2)The particle releases its genetic instructions into the host cell.
3)The injected genetic material recruits the host cell's enzymes.
4)The enzymes make parts for more new virus particles.
5)The new particles assemble the parts into new viruses.
6)The new particles break free from the host cell.

All viruses have some type of protein on the outside coat or envelope that "feels" or "recognizes" the proper host cell(s). This protein attaches the virus to the membrane of the host cell. Some enveloped viruses can dissolve right through the cell membrane of the host because both the virus envelope and the cell membrane are made of lipids.

Those viruses that do not enter the cell must inject their contents (genetic instructions, enzymes) into the host cell. Those viruses that dissolve into a cell simply release their contents once inside the host. In either case, the results are the same.


On the Inside

Once inside the cell, the viral enzymes take over those enzymes of the host cell and begin making copies of the viral genetic instructions and new viral proteins using the virus's genetic instructions and the cell's enzyme machinery (see How Cells Work for details on the machinery). The new copies of the viral genetic instructions are packaged inside the new protein coats to make new viruses.


Once the new viruses are made, they leave the host cell in one of two ways:

1)They break the host cell open (lysis) and destroy the host cell.
2)They pinch out from the cell membrane and break away (budding) with a piece of the cell membrane surrounding them. This is how enveloped viruses leave the cell. In this way, the host cell is not destroyed.

Once free from the host cell, the new viruses can attack other cells. Because one virus can reproduce thousands of new viruses, viral infections can spread quickly throughout the body.


The sequence of events that occurs when you come down with the flu or a cold is a good demonstration of how a virus works:

1)An infected person sneezes near you.
2)You inhale the virus particle, and it attaches to cells lining the sinuses in your nose.
3)The virus attacks the cells lining the sinuses and rapidly reproduces new viruses.
4)The host cells break, and new viruses spread into your bloodstream and also into your lungs. Because you have lost cells lining your sinuses, fluid can flow into your nasal passages and give you a runny nose.
5)Viruses in the fluid that drips down your throat attack the cells lining your throat and give you a sore throat.
6)Viruses in your bloodstream can attack muscle cells and cause you to have muscle aches.

Your immune system responds to the infection, and in the process of fighting, it produces chemicals called pyrogens that cause your body temperature to increase. This fever actually helps you to fight the infection by slowing down the rate of viral reproduction, because most of your body's chemical reactions have an optimal temperature of 98.6 degrees Fahrenheit (37 degrees Celsius). If your temperature rises slightly above this, the reactions slow down. This immune response continues until the viruses are eliminated from your body. However, if you sneeze, you can spread thousands of new viruses into the environment to await another host.


Lysogenic Cycle

Once inside the host cell, some viruses, such as herpes and HIV, do not reproduce right away. Instead, they mix their genetic instructions into the host cell's genetic instructions. When the host cell reproduces, the viral genetic instructions get copied into the host cell's offspring. The host cells may undergo many rounds of reproduction, and then some environmental or predetermined genetic signal will stir the "sleeping" viral instructions. The viral genetic instructions will then take over the host's machinery and make new viruses as described above. This cycle, called the lysogenic cycle, is shown in the figure in the article.

In the lysogenic cycle, the virus reproduces by first injecting its genetic material, indicated by the red line, into the host cell's genetic instructions.

Because a virus is merely a set of genetic instructions surrounded by a protein coat, and because it does not carry out any biochemical reactions of its own, viruses can live for years or longer outside a host cell. Some viruses can "sleep" inside the genetic instructions of the host cells for years before reproducing. For example, a person infected with HIV can live without showing symptoms of AIDS for years, but they can still spread the virus to others.


Reducing the Spread

As discussed above, viruses can exist for a long time outside the body. The way that viruses spread is specific to the type of virus. They can be spread through the following means:

1)Carrier organisms - mosquitoes, fleas
2)The air
3)Direct transfer of body fluids from one person to another - saliva, sweat, nasal mucus, blood, semen, vaginal secretions
4)Surfaces on which body fluids have dried To reduce the risk of spreading or contacting viruses, here are things you can do:

1)Cover your mouth or nose when you sneeze or cough.
2)Wash your hands frequently, especially after going to the bathroom or preparing food.
3)Avoid contact with the bodily fluids of others. These practices are not foolproof, but they can help you reduce the risk of viral infection.


Medicines That Can Help

Contrary to popular belief, antibiotics have no effect on a virus. Most antibiotics interfere with the reproduction of bacteria, hindering their creation of new genetic instructions or new cell walls. Because viruses do not carry out their own biochemical reactions, antibiotics do not affect them.

Immunizations work by pre-infecting the body so it knows how to produce the right antibodies as soon as the virus starts reproducing. Also, because viruses reproduce so quickly and so often, they can often change slightly. Sometimes, mistakes creep into their genetic instructions. These changes might alter the protein coat slightly, so one year's batch of vaccine might not be as effective against the same type of virus next year. This is why new vaccines must be produced constantly to fight viral infections and prevent outbreaks.

You may have heard of outbreaks of Ebola virus or West Nile virus that have left many people dead. Influenza has killed many people in the past (early in the 20th century), and debate rages over when the next major flu epidemic will occur in the United States. Not all viruses are deadly. For example, people get colds all of the time and do not die. However, even these seemingly harmless viruses can be deadly to a person who already has a weakened immune system -- people with AIDS, cancer patients taking chemotherapy, elderly people or newborns. We have to take care not to spread viruses to these especially susceptible people.

http://health.howstuffworks.com/virus-human.htm/printable

Related on this Blog:
http://gonashgo.blogspot.com/2008/01/280no6-ayatssigns-in-universe-series.html



Quotes of Aga Khan IV and Others:

"In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

"The Divine Intellect, Aql-i Kull, both transcends and informs the human intellect. It is this Intellect which enables man to strive towards two aims dictated by the faith: that he should reflect upon the environment Allah has given him and that he should know himself. It is the Light of the Intellect which distinguishes the complete human being from the human animal, and developing that intellect requires free inquiry. The man of faith, who fails to pursue intellectual search is likely to have only a limited comprehension of Allah's creation. Indeed, it is man's intellect that enables him to expand his vision of that creation"(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11, 1985)

"The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims. Exchanges of knowledge between institutions and nations and the widening of man's intellectual horizons are essentially Islamic concepts. The Faith urges freedom of intellectual enquiry and this freedom does not mean that knowledge will lose its spiritual dimension. That dimension is indeed itself a field for intellectual enquiry. I can not illustrate this interdependence of spiritual inspiration and learning better than by recounting a dialogue between Ibn Sina, the philosopher, and Abu Said Abu -Khyar, the Sufi mystic. Ibn Sina remarked, "Whatever I know, he sees". To which Abu Said replied," Whatever I see, he knows"."(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11th 1985)

"The truth, as the famous Islamic scholars repeatedly told their students, is that the spirit of disciplined, objective enquiry is the property of no single culture, but of all humanity. To quote the great physician and philosopher, Ibn Sina: "My profession is to be forever journeying, to travel about the universe so that I may know all its conditions." "(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"In Islamic belief, knowledge is two-fold. There is that revealed through the Holy Prophet (s.a.s.) and that which man discovers by virtue of his own intellect. Nor do these two involve any contradiction, provided man remembers that his own mind is itself the creation of God. Without this humility, no balance is possible. With it, there are no barriers. Indeed, one strength of Islam has always lain in its belief that creation is not static but continuous, that through scientific and other endeavours, God has opened and continues to open new windows for us to see the marvels of His creation"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"Islamic doctrine goes further than the other great religions, for it proclaims the presence of the soul, perhaps minute but nevertheless existing in an embryonic state, in all existence in matter, in animals, trees, and space itself. Every individual, every molecule, every atom has its own spiritual relationship with the All-Powerful Soul of God"(Memoirs of Aga Khan III, 1954)

"Nature is the great daily book of God whose secrets must be found and used for the well-being of humanity"(Aga Khan III, Radio Pakistan, Karachi, Pakistan, February 19th 1950)

"O brother! You asked: What is the [meaning of] `alam [world] and what is that entity to which this name applies? How should we describe the world in its entirety? And how many worlds are there? Explain so that we may recognize. Know, O brother, that the name `alam is derived from [the word] `ilm(knowledge), because the traces of knowledge are evident in [all] parts of the physical world. Thus, we say that the very constitution (nihad) of the world is based on a profound wisdom"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet, from his book "Knowledge and Liberation")

“The physician considers [the bones] so that he may know a way of healing by setting them, but those with insight consider them so that through them they may draw conclusions about the majesty of Him who created and shaped [the bones]. What a difference between the two who consider!”(Abu Hamid Al-Ghazali, Muslim Theologian-Philosopher-Mystic, d1111CE)

"Tarkib' is composition as in the compounding of elements in the process of making more complex things, that is, of adding together two things to form a synthesis, a compound. Soul composes in the sense of 'tarkib'; it is the animating force that combines the physical elements of the natural universe into beings that move and act. Incorporating is an especially apt word in this instance. It means to turn something into a body, as in 'composing'. But it is actually the conversion of an intellectual object, a thought, into a physical thing. Soul acts by incorporating reason into physical objects, the natural matter of the universe and all the things composed of it"(Abu Yakub Al-Sijistani,10th century Fatimid Ismaili cosmologist, d971CE, from the book, 'Abu Yakub Al-Sijistani: Intellectual Missionary', by Paul Walker)

"Every particle of the Creation has a share of the Command of God, because every creature shares a part of the Command of God through which it has come to be there and by virtue of which it remains in being and the light of the Command ofGod shines in it. Understand this!"(Abu Yakub Al Sijistani, 10th century Fatimid Ismaili cosmologist, d971, Kashf al-Mahjub("Unveiling of the Hidden"))

"Here is a relevant verse from the Noble Qur'an, cited by Nasir-i Khusraw, hujjat-i Khurasan in his Khawaan al-Ikhwaan : "It is He who created you from dust, then from a sperm drop, then from a blood clot, then He brings you forth as a child, then lets you reach your age of full strength, then lets you become old - though some of you die before - and then lets you reach the appointed term; and that haply you may find the intellect (la'allakum ta'qilun)."(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet)


The above are 12 quotes and excerpts taken from Blogpost Four Hundred, a collection of around 100 quotes on the subjects of Knowledge, Intellect, Creation, Science and Religion:
http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html



Easy Nash

The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)