I am a Christian. I believe in the God of the Bible, in God the Father, in His Son Jesus Christ, and in the Holy Spirit. I believe in Genesis 1:1 - "In the beginning God created the heavens and the earth. (NIV)" I am a biochemist and a pharmacist by education. As such I have a desire to understand nature. I am writing this blog as my way to express the facts of true science as I understand them, from the perspective of one who believes that all things were created by God, for God and for His purposes.

Feel free to comment, to offer your perspective, or to give suggestions for subjects.
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Sunday, March 25, 2012

The Whole Nine Yards! - Concrete Chemistry

Many years ago I was told that this saying came from the capacity of your typical Ready-Mix concrete truck. But as I researched this blog, I discovered that this was just one of the many proposed origins for this colloquialism. So before we move to the chemistry, lets get "the whole nine yards" on "The Whole Nine Yards."

The phrase "The Whole Nine Yards" means everything, the whole lot, completely or the works. It is a reference to the full measure of something. The origin of the phrase has been described as, "the most prominent etymological riddle of our time" as it is not clearly known how or where the expression came into use. Its first known appearance was in 1962 in a "Michigan's Voices: A Literary Quarterly Magazine" story entitled "Man on the Thresh-hold" by Robert E. Wegner. The quoted line goes like this:

...mad, mad, mad, the consequence of
house, home, kids, respectability, status as a
college professor and the whole nine yards, as a
brush salesman who came by the house was fond of

But how did it come to be there? And what did the brush salesman have to do with it? No one seems to know for sure. There are any number of explanations for the origin of the phrase but none seem to be satisfactory. Here are a few of the more popular ones:

"Nine Yards"
  • Amount of cloth needed for a Scottish kilt, a burial shroud, or a three-piece suit
  • Length of some World War II military artillery (US bombers bomb racks or RAF Spitfire's machine gun ammunition belts)
  • Yardage in American football (but ten yards are needed for a first down)
  • Other types of "yards" (number of properties on a city block, naval shipyards or yardarms on a sailing ship)
  • Capacity of a ready-mix concrete truck, coal truck, or garbage truck (in cubic yards)

So getting back to my initial explanation of "the whole nine yards" as a cubic measure and the volume of a cement mixer. Cement mixers were much smaller in the 1960's (4-6 cubic yards) and none of the early references to the saying relate to concrete or even to construction. It seems rather unlikely that a term from such a specialized field would become so well known. Even the capacity of today’s trucks varies a great deal, and only a few of them actually carry nine cubic yards of concrete.

So in spite of the fact that the phrase is not specifically about concrete mixer capacity, lets look past that and see if we can get "the whole nine yards" on the liquid rock that these mixers supply - Concrete.

Concrete is one of the most versatile
Construction Materials in the World

As a construction material, concrete can be cast in almost any shape, and once hardened, can become a structural or load bearing building element. It is one of the most versatile construction materials available in the world. Concrete should not be confused with cement, because the term cement refers to the material used to bind the materials in concrete. Concrete is a mixture of aggregate, cement and water. Aggregate is generally a coarse gravel or crushed rock such as limestone, or granite, along with a fine aggregate such as sand (Silicon Dioxide - SiO2). Cement is a binder, a substance that sets and hardens independently, and can bind other materials together.

The cement used in concrete is a hydraulic cement (Portland cement) and hardens due to hydration, a series of chemical reactions that occur independently of the mixture's water content, and can harden underwater or when constantly exposed to wet weather. The chemical reaction that results when the anhydrous (dry) cement powder is mixed with water produces hydrates that are not water-soluble. Carbon dioxide is absorbed to convert the portlandite (Calcium Hydroxide - Ca(OH)2) into insoluble calcium carbonate (CaCO3). The constituents slowly hydrate and crystallize and the interlocking of the crystals gives cement its strength. Maintaining a high moisture content in cement during curing increases both the speed of curing, and its final strength. The time it takes for cement to cure varies depending on the contents of the mixture, if gypsum (calcium sulfate dihydrate - CaSO4·2H2O) is added to slow the curing, and the environmental conditions. Initial hardening can occur in as little as twenty minutes, while a full cure can take over a month. Cement typically cures sufficiently to be put into service within 24 hours to a week.

Portland Cement is made by heating limestone (calcium carbonate), in a kiln to 1450°C, with small quantities of clay (alumino-silicates or SiO2) or other materials. This process, known as calcination, liberates a molecule of carbon dioxide from the limestone to produce calcium oxide (CaO), or quicklime. The quicklime is then blended with other materials to make a "clinker." Portland cement clinker is a hydraulic material consisting mainly of calcium silicates (3CaO·SiO2 & 2CaO·SiO2). The clinker is ground, with a small amount of gypsum, into a powder to create Portland Cement, the most commonly used type of cement. Beside concrete, Portland cement is a basic ingredient of mortar and most non-specialty grouts.

Concrete is poured into forms to make almost any design. The forms can be made with wood, metal or plastic but need to be strong enough to hold back the pressure created by the hardening material. Steel screen or rebar (short for reinforcing bar) is frequently used to supply additional tensional strength to the finished concrete. Intricate artwork can be added to the surface using specialized forms or by the use of shaping tools or stamps and by scraping the surface as the concrete dries. Concrete can also be poured into simple wooden molds to make concrete block, one of the most widely used construction materials. Concrete blocks can be easily made on site making them an excellent material for building homes and other structures in remote locations in underdeveloped countries.

If not for the strength of this liquid rock, we would not be able to build much of the backbone of this country - the highways, the skyscrapers, the bridges. Concrete is the foundation of our modern urban infrastructure. A simple but versatile chemical from God's Chemistry Set.

Matthew 7:25 (NIV) - The rain came down, the streams rose, and the winds blew and beat against that house; yet it did not fall, because it had its foundation on the rock.

Psalms 89:14 (NIV) - Righteousness and justice are the foundation of Your throne; love and faithfulness go before You.

Saturday, March 17, 2012

Plants - The Wearin' O' the Green

Happy Saint Patrick's Day! Patrick is the patron saint of Ireland and legend has it that he used the shamrock, or three leaf clover, to teach the people about the Holy Trinity - three Persons in one God. From the symbol of the shamrock comes the "Wearing of the Green" on Saint Patrick's Day. The day is a holy day of obligation for Roman Catholics in Ireland but elsewhere around the world we celebrate by wearing something green, drinking green beer and green shakes and eating green eggs and ham.

Well green seems to be one of God's favorite colors. You can not go into any area of vegetation without seeing a splash of green. Plants obtain their green color from Chlorophyll. Chlorophyll is a green pigment found in almost all plants as well as many algae, and bacteria. Its name is derived from the Greek words chloros ("green") and phyllon ("leaf"). Chlorophyll is a biochemical that is used in photosynthesis to produce energy from the sun. Chlorophyll absorbs light most strongly in the blue and red portions of the electromagnetic spectrum. However, it is a poor absorber of green portions of the spectrum, hence the green color of Chlorophyll-containing tissues.

Chlorophyll a
Chlorophyll is structurally a chlorin ring, with a magnesium ion in the center. Varying side chains are connected, producing several different forms that occur naturally, but the most widely distributed form in terrestrial plants is chlorophyll a.

Chlorophyll is necessary for photosynthesis. Photosynthesis begins when energy from light is absorbed by proteins called photosynthetic reaction centers that contain Chlorophyll. In plants, this occurs inside organelles called chloroplasts. Some of the light energy gathered by Chlorophyll is stored in the form of Adenosine Triphosphate (ATP). The rest is used to turn Carbon Dioxide into organic compounds by a sequence of reactions called the Calvin Cycle. Combining Carbon Dioxide and Water, the Calvin Cycle produces Oxygen and Sugars. Plants thus can produce their own food, and become food for us, while also replenishing the Oxygen we breathe and using up the Carbon Dioxide we exhale. This is the natural symbiotic relationship of animals to plants.


God has set a natural order into our world where all things work together. The fall of man corrupted that perfect natural order but the foundation is still there and can be discovered in Creation if we just open our eyes to see.

1 Samuel 2:8 (NLT) - He lifts the poor from the dust and the needy from the garbage dump. He sets them among princes, placing them in seats of honor. For all the earth is the LORD's, and he has set the world in order.

Thursday, March 15, 2012

Why These Amino Acids? - The Chemistry of Optimized Design

Back last year I wrote two blogs that included information about the Amino Acids and the property of "handedness" or Chirality. Well recently at Reasons to Believe there was an article about why a set of only 20 specific amino acids comprise all the proteins found in every organism on Earth. The article highlights a study from the University of Hawaii looking at this very question and others. A few highlights from the article are included below. Click this link to see the original article.

The set of 20 amino acids used in biology is universal, yet hundreds of amino acids exist in nature. Biochemists want to know why this specific set of 20 amino acids, and not the others, occurs in proteins.

Optimal Amino Acids are
An Example of Intelligent Design

The article attempts to answer this question as well as these other related questions for biochemists:

  • Why are proteins built from amino acids? And not the chemically simpler hydroxy acids?
  • Why are the amino acids in proteins all α-amino acids? Why not β- or γ- or δ-amino acids?
  • Why do all the amino acids in proteins have an α-hydrogen?
  • Why are there no N-alkyl amino acids in proteins?

This work from the University of Hawaii indicates that the set of amino acids used to make proteins is the optimal set. This discovery provides new evidence that life’s chemistry stems from the work of a Creator.

Evolutionary biologists argue that the undirected processes of chemical and natural selection generated the set amino acids used to make proteins. If this is the case, some level of optimization would be expected, but not the extreme optimization just discovered by the University of Hawaii researchers. 

The widespread expectation is that evolutionary mechanisms should produce systems that work “just good enough” for the organism to survive, but are not necessarily as optimized as the set of 20 protein-forming amino acids.

As an alternative explanation for the optimized set of amino acids found in proteins, I propose the work of a Creator. Optimization is an indicator of intelligent design, achieved through foresight and preplanning. It requires inordinate attention to detail and careful craftsmanship. By analogy, the optimized biochemistry, epitomized by the amino acid set that makes up proteins, could be rationally understood as the work of a Creator. 

Excerpts from Reasons to Believe, Why These 20 Amino Acids?, Fazale “Fuz” Rana, PhD, March 12th, 2012.

Job 36:3 (NLT) - "I will present profound arguments for the righteousness of my Creator."

Saturday, March 10, 2012

He Who Has Ears... The Chemistry of Cerumen

"Friends, Romans, countrymen, lend me your ears."

In Mark Antony's famous speech from Julius Caesar, he calls the people to listen closely as he persuades them that Caesar was kind and loving, even towards those who killed him and that Brutus was the real villain. He asks them to "lend their ears" to the true story behind what Brutus had done.

We too must "lend our ears" continually, listening to the many sounds around us to warn us, guide us, and educate us. Without ears our world is silent, missing out on a significant dimension of our existence. It has been said that God gave us two ears and one mouth so that we would listen twice as much as we speak. When He wanted us to understand, Jesus said "He who has ears, let him hear." (Matthew 13:9 and others).

Our ears are a marvelous bit of engineering. Containing the three smallest bones in the body and a slip of skin stretched tightly like a drum, they can pick up sounds ranging from the quiet hum of a bumble bee (3 decibels) to the deafing sound of a jet engine or your favorite hard rock band in concert or coming from the low-rider driving next to you (135 decibels). Our ears have a frequency range of 12 to 20,000 cycles (Hertz), more than one octave above the highest reach of the piano and as low as the lowest notes on a tuba or pipe organ.

Our ears are a marvelous bit of engineering
Picking up sounds ranging from
The quiet hum of a bumble bee to
The deafing sound of your favorite rock band

Our ears also have a well developed means of protection and self cleaning; Ear Wax or Cerumen. CholesterolCerumen is a waxy substance secreted by glands in the ear canal. It is a mixture of thick secretions from sebaceous glands and watery secretions from sweat glands. The primary components of ear wax are shed layers of skin (keratin), saturated and unsaturated long-chain fatty acids, alcohols, squalene and Cholesterol.


Cerumen is designed to clean and lubricate the skin of the ear canal and provide some protection from bacteria, fungi, insects and water. The lubricating properties arise from the high lipid content of the sebum produced by the sebaceous glands. The cerumen cleans the canal as it is carried outwards by jaw movement and the migration of skin cells, taking along with it any dirt, dust or particulate matter that may have gathered there.

Cerumen has a bactericidal effect on some common strains of bacteria known to produce outer ear infections, including Haemophilus influenzae (H flu), Staphylococcus aureus (Staph), and many variants of E coli. It also inhibits the growth of two fungi commonly present in the ear. These antimicrobial properties are due to the presence of saturated fatty acids and particularly to the slight acidity of cerumen (pH around 6.1).

Gregory F. Maxwell - GNU v1.2
Most people should never have to clean the ear canal. However, in some people, the glands produce more wax than can be naturally removed from the ear. This extra wax can harden in the canal and block the ear. More commonly, ear wax may build up if you accidentally push it deeper into the ear canal with inappropriate cleaning, usually when attempting to clean the ear with cotton swabs. Excess or impacted cerumen can press against the eardrum or occlude the canal and thus impair hearing. This wax blockage is one of the most common causes of hearing loss. Excess cerumen can be removed mechanically, using softening agents, such as mineral or olive oil, or most commonly by irrigation of the ear canal with warm water.

Irrigation uses body-temperature water (cooler or warmer water may cause dizziness or vertigo). With your head upright, straighten the ear canal by holding the outside ear and gently pulling upward. Using a blub syringe, gently direct a small stream of water against the ear canal wall next to the wax plug, tipping your head to allow the water to drain. You may need to repeat this several times. After the wax is removed, dry the ear thoroughly. You may use a few drops of rubbing alcohol to help dry the ear. If ear wax still persists, it should be removed by a medical professional.

We must keep our ears clear and attentive to the sounds all around us - the rushing of the wind through the trees, the harmonic hum of the violin, the laughter of family and friends and the "still small voice of God" - 1 Kings 19:12 (NKJV).

Proverbs 23:12 (NKJV) - "Apply your heart to instruction, and your ears to words of knowledge."

God speaks to us and we can hear Him if we will only listen for His voice. He does not yell but speaks quietly with the power of His Grace and Mercy. Lord let me hear Your voice and know the plans You have for me.

Jeremiah 29:11 (NIV) - "For I know the plans I have for you," declares the LORD, "plans to prosper you and not to harm you, plans to give you hope and a future."

Sunday, March 4, 2012

The Top Ten Things that Gimme Shelter

The Late Show Top Ten List is a regular segment on "Late Show with David Letterman." The lists are usually given humorous topics, such as "Top Ten Signs Your Kid Had A Bad First Day At School," or some other twist, such as altering the nature of the list or a reading by a guest presenter, is used in the presentation.

So if David Letterman can have his Top Ten, why not God's Chemistry Set? Well a real good reason would be we are not that funny. David Letterman has a whole team of writers whose jobs are to make his show humorous and entertaining. Here we just have a chemist/pharmacist who is not known for his ability to tell jokes (or write blogs for that matter!). But why not give it a try? What have we got to lose?

"If a man is lazy, the rafters sag;
if his hands are idle, the house leaks."
Ecclesiastes 10:18 (NIV)

Our list is intended to be more factual than funny. There is a little bit of chemistry (or other) truth embedded in each of the ten entries in the list. If I can interject a smidgin of humor I will. Hope you learn a little and laugh a little with this blog. So here goes:

The Top Ten Things That Gimme Shelter (building a structure in the physical)

10) Ice (water) - Igloos - For the Eskimos. Will the houses melt with Global Warming?
9) Fabric (cotton) - Tents - For the Nomad or the Adventurous Wanderer, made with canvas or animal skins. Sometimes they end up blowing in the wind.
8) Glass (silicone dioxide) - For the people that don't throw stones. Lets hope their neighbors don't throw stones either.
7) Straw (cellulose) - Grass huts - In the bush or grasslands. Mice like to make them home as well.
6) Sticks (cellulose) - Wood or brush, thatch roofs. Susceptible to fires.
5) Brick - Cast mud or clay. If not hardened with fire, can wash away in the rain.

The last three were famously recorded in "The Three Little Pigs," an English fairy tale published in The Nursery Rhymes of England (London and New York, c.1886), by James Orchard Halliwell-Phillipps.

"Little pig, little pig, let me come in." (said the big bad wolf)
"No, no, not by the hair on my chinny chin chin." (replied the little pig)
"Then I'll huff, and I'll puff, and I'll blow your house in." (and the wolf did - destroying the houses of straw and sticks)

And of course only the brick house could stand and save the three little pigs from the big bad wolf.

4) Rock - River rock, quarried stone. A tough move from the river to the homestead.
3) Cement (calcium silicates or sulfates) - Concrete, poured or as block, plaster.
2) Lumber (cellulose) - One of the more common constructions today, used to frame the house. Could be used for a log cabin as well.
1) Metal (iron) - Steel, sheet metal, rebar, fixtures, plumbing. Can also be aluminum, copper or other metals.

The Foundation of Life
So what does "Shelter" mean? It is a covering or barrier from the elements - rain, wind, sun as we have listed above, or it could be protection from or help through the physical, emotional and spiritual struggles of everyday life. All of us have burdens in life at some time and from some source outside of ourselves. These could be due to our past, our upbringing or our own failures or physical limitations.

The Rolling Stones sang about shelter back in 1969.
Gimme Shelter - The opening track on the band's album "Let It Bleed."

Oh, a storm is threat'ning
My very life today
If I don't get some shelter
Oh yeah, I'm gonna fade away

The Rolling Stones were singing about the storms of life they saw in 1969. They sang about more than just a physical storm, singing instead about War, Rape, Murder - the difficulties of that day, and our days as well, and the hope of love to calm these storms. But they equated love with a kiss, a physical solution to a deeper problem. The love we need is not a physical action but a Spiritual One - the Love of God. He will comfort us through the storms in our lives. We just need to let Him - Psalm 46:10a (NIV) "Be still, and know that I am God;"

The Love of God is the one and only item we need on our spiritual list of "The Top Ten Things That Gimme Shelter."

Matthew 7:24-27 (NIV) - Jesus said: "Therefore everyone who hears these words of Mine and puts them into practice is like a wise man who built his house on the rock. 25 The rain came down, the streams rose, and the winds blew and beat against that house; yet it did not fall, because it had its foundation on the rock. 26 But everyone who hears these words of Mine and does not put them into practice is like a foolish man who built his house on sand. 27 The rain came down, the streams rose, and the winds blew and beat against that house, and it fell with a great crash."

Here Jesus was talking about His admonition to not judge others, or you too will be judged (Matthew 7:1) and to do to others what you would have them do to you (Matthew 7:12). He tells us we need to search Him out and know Him. We will have storms in our lives, no matter what we do. We need to build the foundation of our lives on the rock. Jesus is our Rock!

Hebrews 3:4 (NIV) For every house is built by someone, but God is the builder of everything.