Category Archives: random thoughts

Secondary Metabolites

By Michael Pickering

Peyote Plants (1)

This name encompasses the category of chemicals that living organisms make which are not used in their normal growth, development, or reproduction.  They are a staggering array of chemical structures and properties.  Antibiotics are largely produced by bacteria, and a large variety of mammalian toxins are of fungal origin.  Pigments are produced by both botanicals and insects.  The peyote cactus, Lophophora williamsii, produces the hallucinogenic alkaloid mescaline.  Fugu, the Chinese puffer fish, harbor symbiotically produced tetrodotoxin.  


Puffer Fish at Japanese Market (2)
The producers of these exotic structures usually must isolate them to keep them out of the traffic of their living processes.  They can interfere with everyday life, or more often are toxic for the producer.  Dalea emoryi (aka dyebush) makes an intense red pigment that it stores in blister-like vesicles on its bark.  Coyotillo shrubs, Karwinskia humboldtiana, make deadly neurotoxins which they store in the seeds, discouraging browsing animals such as cattle, deer, and sheep from eating them. (You can read more about this plant in a previous newsletter:  Coyotillo in Del Rio, Texas)

Lotus scoparius, or deer weed, makes a water-soluble flavinoid, which is a biodegradable germination inhibitor, and stores in its seeds.  Upon first rain, this compound sterilizes the surrounding ground so that no seeds can germinate.  The result is that competitive weed seeds rot.  When the second rain comes, the deer weed seeds germinate with nothing but clear sky surrounding them. 

Sometimes, we can see a competitive advantage of the presence of these chemicals: attracting pollinators, protective insects, or mates, or discouraging predators, competitors, or tramplers.  But often not.  Today’s musings are about two species (an insect and a botanical): Daclylopius coccus and Citrus sinensis. 
"Gusano Rojo", Dactylopius coccus

Red dyes produced by insects have been and remain among the most important dyestuffs in human commerce.  Before the Americas were exploited, the most abundant source of red pigments was the Asian scale insects and their excretions.  This broad class of quinoid dyes bind permanently to proteinaceous substrates (in dye talk they are ‘fast’) such as wool and silk.  Historically, they have also been used as art pigments.

Early in the 16th century, the Spanish introduced the world to the American cochineal, and the Asian scale insects were doomed to a mere historical reference. 

Cacti with Cochineal (3)



Cochineal Cluster (3)

The females of this American species that feeds on cactus provide the popular Latino name “red worm.”  Interestingly, Dactylopius coccus is not actually a worm, but is part of the cochineal family. By dry weight, the females can produce an astounding double digit percentage of pigment.  The pigments have great variation of color and intensity (Carminic Acid extinction coefficient 6800, Laccaic Acid A extinction coefficient 43700).  The commercial growers of the pigment use the cactus Indian Fig Opuntia (Opuntia ficus-indica) to feed the caterpillars, whose fruit and tender young shoots are also popular in Latino diets.  The same insects in a blue agave farm are considered a pest.

Because of the significance of these insect-derived pigments in human history, they are the subject of anthropological study in ancient art.  In 2004, we were invited into the study by the Department of Conservation and Scientific Research of the Smithsonian Institute.  Although the pigments have long wavelength chromophores (little or no interference) and large extinction coefficients, the sample size is only 2-5 ng to minimize damage.  As the pigments are only a small component of the sample, adequate detection requires a post-column reaction to make the pigments fluorescent.  We made them an inert system as the reagent AlCl3 is a powerful reducing agent, which translates as very corrosive to hardware.  During the reaction, the Al3+ reduces the quinone to a hydroquinone, which chelates the spent Al3+ and makes the entire complex fluorescent. 


Oranges, Citrus sinensis

Valencia oranges produces two main bitter principles, Limonin, a terpenoid, and Naringin, a flavenoid, which it mainly stores in its seeds.  The seeds are easily removed when the fruit is harvested for juice.  Lacking seeds, the navel orange must develop a different storage strategy. 
The navel orange stores the Limonin and Naringin as tasteless precursors (at neutral pH) in the peel, concentrated in the vestigial seed, the navel end.  When the orange is juiced, the membranes are torn and spill their contents into the acidic juice.  The acidity catalyzes the hydrolytic elimination of a sugar from a tertiary alcohol and facilitates a ring-closure to form a lactone, the bitter Limonin.  
The tasteless Naringin precursor reacts similarly.
California, and I am sure other commercial orange-producing areas, has strict standards for exportability of the whole fruit, size being paramount.  Thus, the most important commercial value in un-exportable fruit is the juice.  One hundred percent navel orange juice is unpalatably bitter. 

It is my opinion, and I encourage you to compare, that non-specific blended frozen orange juice concentrates contain a noticeable amount of navel orange juice.  Pure Valencia concentrate is available, so do the experiment and voice your opinion.  We will post opinions (with your bylines, or make up a cool avatar name) in the next newsletter.   

Further Reading and Photo Credits:

1) Peyote photo from Wikipedia:

2) Puffer fish Photo by Mikael:
3) Cochineal Photos from Wikipedia:

Bread Rises

SF-SourdoughRising to the Occasion
Michael Pickering

My wife Judy baked bread recently for our annual St. Patrick’s Day luncheon at Pickering Labs.  She’s an excellent baker, and her Irish Soda Bread is a favorite addition to the corned beef and cabbage “traditional” fare.  Soda bread uses baking soda instead of yeast as the rising agent for the dough.  In addition to baking soda, her recipe also calls for flour, salt, and buttermilk.  This is typical for soda bread, as the buttermilk contains the lactic acid required for the ‘rising’ reaction with the sodium bicarbonate. 

Having grown up in Southern California, I have fond childhood memories of another special kind of bread – Salt-Rising Bread.  This denser bread relies on the fermentation of salt-tolerant bacteria in cornmeal.  The cornmeal must be freshly stone ground, and the dry ingredients also include sugar and salt.  The starter is formed as scalded milk is poured over the dry ingredients, and then left to incubate for about twelve hours at 100 or so degrees.  Despite its name, salt is a relatively minor ingredient in the bread. 

The Van de Kamp’s bakery had a rich history which straddled my own childhood and years living in the greater Los Angeles area.  Although the bakery was originally sold by the Van de Kamp family back in the 1950’s when Theodore Van de Kamp died, the Dutch windmill style bakeries and fresh salt-rising bread remained a warm memory for many of us Southern California children.  When accompanying my mom to buy our bread, I was treated on more than one occasion to a free windmill toy and a cookie. 

By the mid-1970’s, the Van de Kamp bakeries had stopped baking the salt-rising bread I grew up on, but by that point I had left Southern California and moved up to the Bay Area, a region where the Van de Kamp bread had been seldom offered and shortly went out of business.  However, in San Francisco, sourdough bread reigned supreme and had since the California Gold Rush.

Sourdough bread also uses natural microbes as a rising agent, but the longer fermentation of the starter allows the Lactic Acid produced by the Lactobacillus to give the bread a uniquely sour taste.  Naturally occurring yeasts such as Saccharomyces exigua and Saccharomyces cerevisiae also participate in the rising.  Sourdough yeasts work slower than today’s packaged yeasts, increasing the time needed for fermentation to multiple days.  San Francisco sourdoughs are usually kept closer to 70 degrees and often need a week to become stabilized.

Flour and water are combined in the starter, and various methods for introducing micro-organisms and stabilizing the dough are used.  Often times, boiled potatoes are used to help increase the activity of the bacteria.  Creating a sourdough starter is a baker’s science, and each recipe is unique and starter closely monitored.  As a result, bakers are often using “mother dough” that is many years old.  Some bakeries, such as the Boudin Bakery, are able to trace their “mother dough” back to the Gold Rush era. 

During the 1980’s, as modern food processes and general business consolidation trended, San Francisco bakeries fell into the hardship of competition with prepackaged bread.  Smaller bakeries were driven out of business, and the long-term survivors tended to be the larger bakeries with well-established distribution channels.  I moved to Oregon during this time, and my observations upon returning to the Bay Area some years later made it clear that there was a stark change in the availability of good local sourdough bread.  Fortunately for my family, Judy was at the peak of her baking heyday during this time and we were seldom lacking in good bread around my house!

Fast forward to now, and the artisan bread movement has brought back the ability to purchase good, hand-made loaves of bread.  Specialty bakeries have been started and thrive in high numbers.  Even restaurants and grocery stores are taking the time to bake their own bread.  I personally continue to feel that no sourdough of modern San Francisco origin can compete to the distinct sour taste and texture of earlier days, but there is no Pickering starter dough dating back to 1970 lurking in my refrigerator, so I make do with what’s available.  It is my sincere hope that the continued evolution of artisan bread, gastronomy, and the souring culture will ultimately recreate my ideal sourdough again soon. 

Until then, at least we can look forward to St. Patrick’s Day each year, when Judy will rise to the occasion and bake a unique bread to treat us all again!