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.

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Saturday, January 28, 2012

A Sack Half Full - Cancer and Chemotherapy

I found out recently that an old friend I had not seen in years had testicular cancer. He was treated with chemo and surgery and he wrote a book, A Sack Half Full, about the experience. He wrote the book to share with others the struggles and the life altering revelations that such an intense experience brought into his, and his family's, life. He wrote it to help those going through a similar life crisis gain hope and encouragement. He wrote it with humor and humility, with honesty and grit, and with faith in God for His provision. He wrote it from a perspective of how his illness affected those around him, those he loved. He wrote it because he could - because by the grace of God and Chemotherapy - he lived. It is a touching story of the intimate thoughts and actions of a man going through the rigorous trial that is cancer.

"A Sack Half Full" by Jerry Duprez
A story of one Family's Journey
through Testicular Cancer

Jerry was only given a 30% chance of survival. He had "Stage Toast" cancer as he called it. The cancer had moved from his testicle to his abdomen and he was at Stage 3. The tumor was large and required chemotherapy to arrest the growth before surgery could even be considered. Initial chemotherapy is designed to shrink the primary tumor, thereby rendering local therapy (surgery or radiotherapy) less destructive or more effective. Cancer chemotherapy is designed to stop, and kill, rapidly growing cells in the body - cancerous or not. There are no medications that can target just a cancer cell though current pharmaceutical research is pursuing just such a drug vigorously.

Since chemotherapeutic agents act by killing cells that divide rapidly, one of the main properties of most cancer cells, it also harms cells that divide rapidly under normal circumstances: cells in the bone marrow, digestive tract, and hair follicles. Thus the most common side-effects of chemotherapy are myelosuppression (decreased production of blood cells, including white cells so also immunosuppression), mucositis (inflammation of the lining of the digestive tract), and alopecia (hair loss). Jerry dealt with them all.

Jerry was treated with the three gun approach; Cisplatin, Etoposide, and Bleomycin.

Cisplatin is a chemotherapeutic agent containing Platinum. Platinum complexes react in the body by binding to DNA and causing crosslinking between the strands, interfering with cell division by mitosis. The damaged DNA elicits DNA repair mechanisms, which in turn activate apoptosis or programmed cell death when repair proves impossible. Thus cisplatin works most vigorously in cells that are dividing and replicating.

Etoposide exploits the normal mechanism of action of the enzyme topoisomerase II, which aids in DNA unwinding, and by doing so causes DNA strands to break. Rapidly dividing cancer cells rely on this enzyme more than healthy cells so are targeted by the drug. Etoposide forms a complex with DNA and the topoisomerase II enzyme, preventing re-ligation of the DNA strands. This causes errors in DNA synthesis and promotes apoptosis of the cancer cell.

Bleomycin is a glycopeptide antibiotic produced by bacteria. It is a family of structurally related compounds.
When used as an anticancer agent it is primarily bleomycin A2 and B2. It works by causing breaks in DNA. Bleomycin chelates metal ions (primarily iron), reacting with oxygen to produce free radicals that cleave DNA. The most serious side effect that can happen when you take this medicine is that it can cause scarring of the tissue in your lungs (pulmonary fibrosis).

All three drugs affect the normal actions of DNA in the division and replication of cells. This in turn results in cellular damage and death. In Jerry's case he had two means of defeating his cancer, the action of these drugs and the prayers of the faithful. Friends, Family and Churches bent a knee to pray for his recovery. After his surgery to take out the tumor, now shrunk to half the original size, the report showed that everything was clear; no cancer detected. It was a miracle, the tumor was completely dead, just scar tissue, something the doctors did not expect. The prayers and the chemo had achieved the ultimate cancer free victory.

In all of this Jerry and his family found meaning by letting go and letting God. As Jerry states in the book "The following two verses (below), when put together, plus the peace of God’s presence in the cancer struggle, gave me a sense that I didn’t have to understand it all now. It just didn’t hold the value or importance to me anymore—just a valley before a mountain."

James 1:2-3 (NIV) says, “Consider it pure joy, my brothers, whenever you face trials of many kinds because you know that the testing of your faith develops perseverance,” and Romans 5:3b–5a (NIV) says, “Suffering produces perseverance; perseverance, character; and character, hope. And hope does not disappoint us.”

Friday, January 20, 2012

Arsenic and Old Lace

For the clan known as Brewster insanity runs in the family. Two dear sweet old aunts take it upon themselves to end the presumed suffering of lonely old bachelors by serving them elderberry wine spiked with Arsenic, strychnine and "just a pinch of cyanide". The bodies are buried in the basement by bugle-blowing brother Teddy, who believes he is digging locks for the Panama Canal and burying yellow fever victims. Nephew Mortimer has just gotten married, and is trying to negotiate his way around the shenanigans of the house, while trying to keep his new bride from fleeing. He also worries that he will go insane like the rest of the Brewster family. As he puts it, "Insanity runs in my family, practically gallops!".

Cary Grant stars in "Arsenic and Old Lace", an energetic comedy-farce of a film from director Frank Capra (1944). It is a madcap look at romance and the lack of it with old maids burying grumpy old men murdered by poisoning, with Arsenic no less.

Arsenic is notoriously poisonous
and poses a threat around the world
as a contaminant in drinking water

In spite of the comedy from the movie, Arsenic is notoriously poisonous and poses a threat around the world, being used as an undetectable poison, and found contaminating drinking water and apple juice. A Consumer Reports study, including tests of apple and grape juice, found that roughly 10 percent of the juice samples had total Arsenic levels that exceeded federal drinking-water standards. Most of that Arsenic was inorganic Arsenic, a known carcinogen. Mounting scientific evidence suggests that chronic exposure to Arsenic and Lead, even at levels below water standards, can result in serious health problems.

Arsenic has been known and used since ancient times. Aristotle makes reference to Sandarach (Arsenic Trisulfide) in the 4th century B.C. It was frequently used for murder due to its incredible potency and discreetness; Arsenic Trioxide is a white, tasteless and odorless powder that left no traceable (at the time) elements in the body. Arsenic has been called the Poison of Kings and the King of Poisons due to its use by the ruling class to murder one another. It was a favorite murder weapon in the Middle Ages among ruling classes in Italy. Notable deaths by Arsenic poisoning include King George III of Great Britain, Napoleon Bonaparte, and American explorer Charles Francis Hall. It can now be detected by the Marsh Test, a sensitive chemical test for its presence.

Arsenic is a metaloid element with the symbol As and atomic number 33. Arsenic occurs in many minerals, usually with sulfur and metals, but also as a pure elemental crystal. In 1649 Johann Schroeder discovered Arsenic, publishing two ways of prepare the elemental metal.

The main use of metallic Arsenic is for strengthening alloys of copper and especially lead (as in car batteries). Arsenic is used in semiconductor electronic devices, and gallium arsenide is the most common semiconductor in use after doped silicon. Arsenic and its compounds, especially the trioxide, are used in the production of pesticides (treated wood products), herbicides, and insecticides.

For decades, Arsenic was used as a preservative for pressure-treated lumber commonly used in decks and playground equipment. In 2003 that use was banned but the wood continues to contribute to Arsenic in groundwater when it is recycled as mulch. Increased public exposure to Arsenic still exists as the United States has used roughly 1.6 million tons of it for agricultural and other industrial uses with about half of that cumulative total being used since only the mid-1960s. Arsenic based insecticides were widely used in cotton fields, orchards, and vineyards until they were banned in the 1980s. But residues in the soil still contaminate crops. Today the quantity of Arsenic released into the environment in the United States by human activities is three times more than that released from natural sources.

Inorganic Arsenic is a carcinogen known to cause bladder, lung, and skin cancer in people and to increase risks of cardiovascular disease, immunodeficiency, and type 2 diabetes. Use of organic Arsenic in agricultural products has also caused concern. In 2006 the EPA took steps to stop the use of herbicides containing organic Arsenic because of their potential to turn into inorganic Arsenic in the soil and contaminate drinking water. As recently as 2011, working with the FDA, the drug company Alpharma suspended the sale of Roxarsone, a poultry-feed additive, because it contained an organic form of Arsenic that could convert into inorganic Arsenic inside the bird, potentially contaminating the meat or contaminating the soil when the droppings are used as fertilizer.

Arsenic may have been the villain in a 1944 classic but today it poses a threat to millions everywhere, most notably in contaminated drinking water in developing nations. Even with increasing limits on its use, it will take decades to bring the amount of exposure down to safe levels.

James 3:8 - "But no man can tame the tongue. It is an unruly evil, full of deadly poison. (NKJV)"

Sunday, January 15, 2012

The Crystal Blue Persuasions of Cobalt

Back in June of 1969 I had just graduated high school, the Jesus movement was building and Tommy James and the Shondells came out with a new hit single, "Crystal Blue Persuasion."

Look over yonder
What do you see?
The sun is a'rising
Most definitely
A new day is coming, Ooh ooh

People are changing
Ain't it beautiful
Crystal blue persuasion

Better get ready
To see the light
Love, love is the answer, Oooh ooh
And that's all right

So don't you give up now
So easy to find
Just look to your soul
And open your mind...

Maybe tomorrow
When He looks down
On every green field
And every town

All of His children
And every nation
They'll be peace and good brotherhood

Crystal blue persuasion, Yeah
Crystal blue persuasion, Aha
Crystal blue persuasion...

"Crystal Blue Persuasion" as written by James/Gray/Vale
Lyrics © EMI Music Publishing
Lyrics powerd by LyricFind

Many considered it a drug song, since Tommy James had been a user, but he was clean by then. By his own admission it was inspired by his then recent conversion to Christianity and reading in the Book of Revelation about the coming of the New Jerusalem.

Revelation 21:10-11 - "And he carried me away in the Spirit to a mountain great and high, and showed me the Holy City, Jerusalem, coming down out of heaven from God. 11It shone with the glory of God, and its brilliance was like that of a very precious jewel, like a jasper, clear as crystal. (NIV)"

A rare blue Jasper would represent peace and tranquility. James was also inspired by his reading in the Book of Ezekiel where it speaks of the Shekinah Glory of the Almighty God and in Isaiah where it speaks of a brotherhood of mankind living in peace.

Isaiah 54:13 - "All your children shall be taught by the LORD, and great shall be the peace of your children. (NKJV)"

Like many in his day and many still today, he hoped for peace and harmony among all of God's people. He saw the world changing due to the power of God.

Cobalt forms two brightly colored mineral oxides
Cerulean Blue and Cobalt Blue

Now the element Cobalt creates its own Crystal Blue persuasions, forming two bright blue mineral oxides - one with Tin, Cerulean Blue (Cobalt Stanate: Co2SnO4) and a second more brilliant one with Aluminum, Cobalt Blue (Cobalt Aluminate: CoAl2O4). In 1802, Louis Jacques Thénard discovered Cobalt Blue.

Cobalt Blue is used to produce stained glass and is particularly known for its use in Bristol Blue Glass which has been made in Bristol, England since the 18th century. Cobalt compounds have been used for centuries to color porcelain, glass, pottery, tile and enamel. These two varieties of Cobalt Oxides are used as pigments because of their superior stability.

Since the Middle Ages smalt, a blue colored glass, has been used as a pigment. Smalt is produced by melting a mixture of the mineral smaltite (cobalt iron nickel arsenide: (Co,Fe,Ni)As2), quartz and potassium carbonate. Miners had long used the name "kobold" ore (German for goblin ore) for these blue-pigment producing minerals; so named because they contained very little of the known metals and gave off poisonous arsenic-containing fumes when smelted. Smelting yields the dark blue silicate glass smalt, which is then ground to create the blue pigment. Smalt is widely used for the coloration of glass and as a pigment for paintings. In 1735, kobold ores were found to be reducible to a new metal (the first discovered since ancient times), and this metal was ultimately named Cobalt.

Elemental Cobalt is represented by the symbol Co and has an atomic number of 27. It is found naturally only in chemically combined forms. The free element, produced by reductive smelting, is a hard, lustrous, silver-gray metal. The main source of the element is as a by-product of copper and nickel mining.

Cobalt is a ferromagnetic metal, one of only three (Fe, Ni, Co), and is used in the preparation of magnetic, wear-resistant and high-strength alloys. Cobalt occurs naturally as only one stable isotope, Cobalt-59. Cobalt-60 is a commercially important radioisotope, used as a radioactive tracer and in the production of gamma rays. Cobalt-60 is used to treat some forms of cancer and as a medical tracer. It has a half-life of 5.27 years.

Cobalt-based superalloys consume most of the produced cobalt. These alloys are used in gas turbines and jet aircraft engines. Cobalt-based alloys are corrosion and wear-resistant and have been applied in the medical field, along with Titanium, for orthopedic implants. Cobalt also plays a role in both Nickel and Lithium based battery chemistries.

Cobalt is essential to all animals, including humans, as an "ultratrace" mineral. It is carried in the body as cobalamin, also known as vitamin B12. Bacteria in the guts of ruminant animals convert cobalt salts into vitamin B12, a compound which can only be produced by bacteria. Vitamin B12 is the largest and most complex vitamin molecule currently known to man. Deficiency of cobalamin can lead to anemia, fatigue, mania, and depression. Long term deficiency causes permanent brain and central nervous system damage. Dietary sources include fish, shellfish, beef, cheese and eggs.

Cobalt, in its brilliant sea and sky colored salts, paints a picture of our own crystal blue planet floating quietly through space. It is essential for life and provides us with energy and power in batteries and superalloy metals. Although relatively unknown chemically, it impacts our lives for the better every day.

Revelation 22:1 - "And he showed me a pure river of water of life, clear as crystal, proceeding from the throne of God and of the Lamb. (NKJV)"

Sunday, January 8, 2012

Maya Blue - Will It Outlast the Calendar?

So what are your plans for the year now that there will not be another New Year? Or another Christmas. And the guy who gets elected in November won't get inaugurated in January. How can I say that you ask? Well haven't you heard that the Mayan Calendar ends on December 21, 2012? And with it doesn't the World come to an end as well?

Well not really from what most experts on the Mayan civilization tell us. The Mayans had a number of different types of calendars, some for the seasons, some for lifespans and one for very long periods of time called the Long Count calendar. December 2012 marks the conclusion of a b'ak'tun — a time period in the Mayan Long Count calendar. The Long Count calendar counted in units of twenty, 20 days made a uinal, 18 uinals (360 days) made a tun, 20 tuns made a k'atun, and 20 k'atuns (144,000 days or roughly 394 years) made up a b'ak'tun.

The b'ak'tun ending on December 12, 2012 is significant in that on the Mayan Long Count calendar, the previous world (the third) ended after 13 b'ak'tuns, or roughly 5,125 years. According to Mayan history, we are living in the fourth world and this current b'ak'tun is the thirteenth since the beginning of the this world. But none of that means it will end. There are examples of the Long Count with much longer times, including one showing a time 3 quintillion times the age of the universe as now calculated by scientists, over 41 octillion years (41 with 28 zeros following). So I would not start the party yet.

But the Mayas did discover something that is still hanging around, long after most of its contemporaries have faded away. That discovery is Maya Blue. Maya Blue is a brilliant and long-lasting pigment that graces scores of Mayan sites. The vibrant sky color can still be seen today on pottery, murals and other artifacts produced by the Maya people centuries ago.

The Maya created their remarkable pigment by combining indigo dye (from the plant Indigofera suffruticosa, commonly known as Anil) with a clay mineral called palygorskite. The clay binds the dye and creates a durable blue paint. Palygorskite is an aluminum-magnesium-silicon clay also used by the Maya for its medicinal properties. While scientists have long known that Maya Blue is produced by chemically binding indigo to palygorskite with heat, it was only recently (1993) that scientists discovered how the Maya may have produced it.

Indigo - the same dye used to produce blue jeans

It is now thought that the Mayas made their paint by heating three healing elements: palygorskite, indigo and copal incense, an incense made from tree resin whose smoke the Maya believed nourished the gods. The incense acted as a binding agent, bonding the indigo to the clay. The Mayas gave this blue color of water a special place in their lives. It appeased their rain god Chaak. They used it to paint the humans they sacrificed to invoke rain. The Maya would paint unlucky people Maya Blue and throw them down a sacred well or cenote as human sacrifices. The paint was made on the spot as part of the sacrificial ritual.

Maya Blue requires the ingredients, the indigo plant and palygorskite ore, to be heated to temperatures between 150o and 200oC (300o and 400oF). This process of embedding the indigo into the clay makes the color stable and this thousand-year-old pigment has proven immune to the passage of time even under exposure to harsh climate, erosion, alkali, nitric acid and organic solvents. The application of heat to the mixture may have been completed in a kiln built for that purpose but archeological findings suggest that Maya Blue may also have been made as a by-product of burning copal incense at ritual ceremonies.

When the Sacred Cenote at Chichén Itzá was first dredged in 1904, researchers found a 14-foot thick layer of blue residue at the bottom, but didn’t understand its origin. Now scientists know it formed from years of blue-painted sacrifices thrown into the well. During its heyday, Chichén Itzá was a thriving city. Even after the city collapsed, ancient Maya would make pilgrimages to the site to offer sacrifices. Now tourists flock there to see the cenote and the giant step pyramid temple dedicated to Quetzalcoatl, the feathered serpent god. In 2007, the site was designated one of the New Seven Wonders of the World.

Concerning the End of Time Jesus said:
No one knows about that day or hour,
not even the angels in heaven, nor the Son,
but only the Father. Matt 24:36

In spite of the predictions it is doubtful that the world will end this year and Maya Blue will probably remain vibrant on the ruins for years to come. Jesus Himself told us that we should be watching for the signs of His coming but the beginning of those signs were famines, earthquakes, wars and rumors of wars (Matthew 24:6ff NIV), not the supposed end of a calendar. The real end will not come until His "gospel of the kingdom is preached in the whole world as a testimony to all nations Matthew 24:14 NIV". But even then Jesus said: "No one knows about that day or hour, not even the angels in heaven, nor the Son, but only the Father. Matthew 24:36 NIV."

Wednesday, January 4, 2012

Chemical Formula Funnies

Chemists seem to have very dry personalities. Working with formulas all day just does something to the mind. But every now and then we can break out with a little touch of humor. Back in the day, which for me was the early 70's when I was in college, one of my chemistry professors shared a few chemical formula funnies with his class. I don't know why but they have stuck with me for these many years and still bring a smile to my face when I think of them. Seems strange I know but then, I am a chemist at heart.

Even Chemists are good for a Laugh now and again

So today I want to share a few of these formulas with you. These all circle around the chemical benzene. Now benzene is a six carbon ring with three double bonds and has a chemical formula of C6H6. It is naturally found in crude oil, and is one of the most basic of petrochemicals. Benzene is an aromatic, cyclic hydrocarbon, a colorless and highly flammable liquid with a sweet smell.

Chemically its formula is drawn like this:
Benzene is the basis for many other compounds, including many resins and plastics. It is used to make nylon as well as many drugs, even one we looked at here before, Aspirin.

Now bear with me on this. The following chemical formulas are derived from benzene but do not exist in the physical world. They are interesting, nonetheless.

The first one is for our German chemists who have a knack for fine engineering.

A high quality compound indeed. Very safe and travels well on the Autobahn.

The next one can be found around the world but was originally seen in public on June 21, 1893, at the World's Columbian Exposition in Chicago, Illinois. In its chemical rendition it is a benzene ring with iron atoms in place of the hydrogen (chemical formula C6Fe6). Now iron is a chemical element with the symbol Fe (from Latin: ferrum) and one of its oxidation states (Fe2+) is called Ferrous. This chemical is a fun ride and can give you an exhilarating feeling and a great view from the top.

Another facet of the benzene structure is related to how other branches can link off the main ring when a hydrogen is replaced by a carbon. This is shown in the three possible isomers for xylene, also known as dimethylbenzene. If the two methyl groups are adjacent, then it is called an "ortho-" configuration. If they are diametrically opposed, they are "para-" and if spaced one carbon apart then they are considered in the "meta-" position.

Now consider the atomic positions mentioned above. In the last pair of benzene structures we see two compounds with medical backgrounds. The doctors (MDs) shown form a rather confused medical group.

If I have a choice, I would go to the doctors in the "Orthodocs" group because they are such straight thinkers. The "Paradocs" group scares me a little as I would expect their diagnosis to contradict the other doctors and their treatment plans to defy all reason and logic.

Well so much for a lighthearted look at chemists and a number of unusual chemical structures. Hope they stimulated your neurons enough to produce at least a small chuckle.

Proverbs 17:22a - "A merry heart does good, like medicine. (NKJV)"