A fitting final installment in the spices of mince pies, allspice’s name hails from its blending scent characteristic of cloves, nutmeg, and cinnamon. Allspice, however, is its own spice and comes from the Myrtaceae family (like cloves and others in this series), in the genus Pimenta. The Pimenta dioica tree is related to bay laurel, and, similarly, the leaves are used in cooking (but removed before serving or eating). Like cloves, allspice is versatile and can be used in both sweet and savoury cooking. Having it’s origins in Jamaica, we find it featuring in the cuisine of the island.

The fruit from the Pimenta dioica is dried into peppercorn-like berries and when distilled into an essential oil, eugenol is a key volatile (along with caryophyllene and methyleugenol). A nice summary of its chemistry is here.

As with the other spices, allspice is best ground fresh. While we’re at it, here’s a nice holiday spice guide. Next week, continuing with the mincer theme, the fruits of mince pies!

Clove oil can come from the leaves, the stem, or buds. This results in tremendous variability across the type of oil, variation in the spice (time of harvest etc), and extraction methods. But, like nutmeg and mace, eguenol ranks high on the volatile list. Since the buds are most commonly used in cooking and baking (and what we use in mince pies), we’ll focus on them. In addition to eugenol, other significant volatiles include eugenyl acetate and beta caryophyllene. Methylamlketone, methylsalicylate, alpha and beta humulene, benzaldehyde, beta ylangene, and chavicol are found in smaller amounts but impart the pleasant aroma of cloves to the nose.

Cloves are actually quite nutritious and provide manganese, dietary fiber, vitamin C,  omega-3 fatty acids, calcium, and magnesium. Cloves have health benefits from the eugenol as anti-toxin,anti-inflammatory, and mild anti-baterial agent (I love my clove and fennel toothpaste and foot deodorizer!). As with the other spices, cloves are best when ground fresh as the powdered form lose flavour fast. When pressure is applied to the clove bud, a small amount of oil is released if the clove is fresh. Another freshness test is floating the clove in water–the oil provides buoyancy. However you use them, keep them dark and dry and airtight and enjoy!

Nutmeg has a storied economic history. Romans travelled to the spice islands to trade for nutmeg and other spices. Arabs took over this spice trade in the 6th century and, at one point, nutmeg was used for warding off the plague. Nutmeg even has an illicit history as a cheap high during a drug drought–it was Nostredamous’ drug of choice!

Nutmeg is used ground in baking (though fresh grated is best) and also an essential oil, and nut butter. The oil is the most commonly used variety in the taste and fragrance industries (including Coca Cola). Its major compounds are: 50% sabinene OR camphene (and derivatives), 20% d-Penine, and the remaining 30% a mix of chemicals including terpenes, esters,  myristin (the purported hallcinogenic agent) and eugenol. Sabinene confers the spicy quality to nutmeg and camphene has tremendous industrial value (for itself and as a precursor to other chemicals). D-pinene can be used to manufacture camphor (a previous Smell of the Week). Eugenol, though found in smaller quantities in nutmeg, is one of the major volatile components of the seed and is used for making vanillin and also as a substitute for cloves (next week’s smell!) in perfume-making.

Ground nutmeg loses flavour rapidly. So, when cooking or baking with nutmeg (as with cinnamon) always grate from the seed, which can be kept indefinitely.

Humans produce different isoforms of alpha amylase in saliva and the pancreas. During mastication of starchy foods (such as the potato), amylase begins to break the starch into glucose and maltose. (This causes activation of sweet taste receptors.) A paper by Perry et al. (2007) reported finding variation in CNVs for amylase that had an apparent correlation to diet. The authors tested variation in human populations with low (Biaka and Mbuti, Datog, and Yakut) and high (Europeans, Japanese, Hadza) starch diets  and cross-tested these findings on non-human primates. While our close Pan relatives (chimps and bonobos) and New World Monkeys had low copy numbers (expected due to high fruit consumption), starch consuming primates (some Old World Monkeys) had high copy number. The authors propose this emerged early in our hominin lineage and allowed us to diversify our diet beyond reliance on sugar-rich foods (e.g., fruits) to include starchy plants. But, low levels of nucleotide sequence divergence (compared to chimps) suggest a more recent origin for the CNV; however, testing more human groups for variation may push this date back. Positive selection arguments include:

First, a significant amount of starch digestion occurs in the mouth during mastication¹⁴. For example, blood glucose levels have been shown to be significantly higher when high-starch foods such as corn, rice, and potatoes (but not apples) are first chewed and then swallowed, rather than swallowed directly¹⁵. In addition, it has been suggested that oral digestion of starch is critically important for energy absorption during episodes of diarrhea⁴. Diarrheal diseases can have a significant effect on fitness; for example, such diseases caused 15% of worldwide deaths among children younger than 5 years as recently as 2001¹⁶. Lastly, salivary amylase persists in the stomach and intestines after swallowing¹⁷, thereby augmenting the enzymatic activity of pancreatic amylase in the small intestine. Higher AMY1 copy number and a concomitant increase in salivary amylase protein level are therefore likely to improve the efficiency with which high-starch foods are digested in the mouth, stomach, and intestines, and may also buffer against the potential fitness-reducing effects of intestinal disease.

This variation among and within human groups generates interesting questions relative to nutrition and starch intake. Firstly, those with increases in copy numbers are more efficient at digesting and this leads to perceptual variation in starch viscosity, which in turn may influence starch intake. As suggested in the Perry article, increased amylase production may confer an advantage to reproductive fitness in evolutionary history and episodes of weaning diarrhea. But, in modern populations, increased/rapid starch digestion has obvious links to diabetes and obesity. Indeed, a diabetic individual does not have sufficient insulin to catalyze starches after a meal and suffers negative health consquences. Anti-amylases (e.g., white beans) aid in slowing this process by blocking the enzyme and allowing the limited insulin in the system process simple sugars first.

A final note to consider is the potential use of elevated amylase as a stress test. Some studies have found an increased production of salivary amylase in response to stressful situations (physical or psychological). A review of these studies finds there much work to be done but argue that perhaps an explanation for the short-term increases may be part of the flight/fight response:

short-term increases may be useful to the body in that energy is made available by increased digestive action in response to stress. Physiological stress reactions comprise orchestrated actions throughout the body, putting the organism in a state of overall preparedness to engage in fight or flight. Thus, increases in amylase activity may be one of many actions involved in activating the body’s resources to cope with stressful events or threats to homeostasis. However, this explanation applies only to reactions to short-term, acute stressors. Further studies are needed to examine long-term changes in sAA concentrations.

In light of the potential population specific CNV, any alpha amylase test would have to be carefully designed to account for human variation. Certainly, the linkages between a resource-stressed environment and increased production of amylase have potential fascinating paleo-physiological connections even without an increase in copy number.

Cinnamon comes from the bark of many Cinnamomum trees from SE Asia. Chinese cinnamon or cassia (Cinnamomum aromaticum) is often sold as cinnamon (in the US) but ceylon cinnamon (Cinnamomum verum) is the true cinnamon. Cassia has a rougher bark (as opposed to the layered bark of true cinnamon–see above left for cinnamon and right for cassia bark). Cassia is often preferred in curries.

The key volatile  in the essential oil is eugenol and in the bark, cinnamaldehyde. Of these, cinnamaldehyde is the odor compound we associate most with cinnamon. Eugenol is the clove-like odor component: eugenol is named after the clove genus, Eugenia. In addition to fragrance, eugenol may be used for antiseptic purposes.

Another compound found in cinnamon (among a few other plants) is coumarin, which is moderately toxic to humans and very toxic to our (primates) close evolutionary relatives, rodents. Coumarin imparts a fresh grassy odor to fragrances. High concentrations of coumarin impart a bitter taste in plants that deter foragers. Interestingly, humans are sensitive to bitter taste, an evolutionary adaptation to avoid plants such as these that may be toxic. In the case of coumarin, the liver and kidneys are affected, but only in high doses.

Not only are there many trees that may produce cinnamon, synthetic versions are be made with powdered beechnut husk laced with cinnamaldehyde. So as we approach the holidays, bakers and chefs beware that you buy the true cinnamon (or cassia depending on your culinary needs) to grind yourself and not a cheap substitute!

Indigenous to Europe, peppermint is actually a hybrid of Mentha aquatica andMentha spicata (spearmint). As a hybrid, it is sterile and spreads via it’s rhizomes (budding new plants off the roots). Medicinally, peppermint is used as an anti-spasmodic (digestive distress) and/or an anti-nausea (when inhaled). Menthol from mint plants is commonly used in cold medicines (and cigarettes) for soothing sore throats due to its anti-irritant properties. The menthone in peppermint is a natural pesticide (mainly for honey bees).

Major odor compounds are menthol (a primary compound), menthone, methyl acetate, menthofuran, and trace amounts of eucalyptol. Isolated menthol looks just like it smells–like icy shards (see left in the bowl).  Menthol comes from any member of the mint family but the one most commonly used for extraction is Mentha arvensis. Non-natural sources of menthol supplement those from the mint family of plants. Derived from menthol, menthyl esters are used in perfumery to improve, enhance, or modify fragrances. Peppermint oil odor can also be used to detect plumbing leaks!

A study published in the Journal of Agriculture and Food Chemistry found that the volatiles in coffee berries themselves (the study used Coffea arabica, or Columbia) are dominated by high levels of ethanol, except overripe berries which are dominated by esters (as might be expected with any overripe fruit). Interestingly, the largest number of chemical compounds were detected in the overripe berries.

Another study published in 1960 on the volatiles of roasted and ground coffee found 158 compounds. When added to previously identified volatiles, the number jumped to 318, suggesting that coffee aroma is too complex to be fully captured by a few key odors. Half a century later, the problem of finding key volatiles persists. Two studies published in 2010 (in Chemometrics and Intelligent Laboratory Systems and in Analytical Chemistry) noted that the trouble is the high number of volatile peaks that occur when analyzing the compounds–roughly 300 volatiles in green beans to over 1000 in roasted beans. Coffeeresearch.org compiled data for what might be the strongest contribuuters to aroma, noting that furans have a dominant role and contribute the caramel-like note in many coffees.

“A coffee’s aroma will vary as a function of changes in soil, microclimate, altitude, types and species of bean used, the roasting process, and the preparation of the coffee. These various conditions affect the concentration and composition of the various aroma volatiles, which include carboxylic acids, alcohols, aldehydes, alkanes, alkenes, aromatics, esters, furans, ketones, lactones, oxazoles, phenols, pyridines, pyrazines, pyrroles, thiazoles, and thiophenes.”–from the 2010 Analytical Chemistry publication above by Susslick

Such a complex odor that creates a person-specific experience…however and whenever you like your coffee, take a moment to appreciate it’s complex nature that has stymied normal methods of detecting and synthetically creating odors.

Clandestine trysts or common practice? The draft sequence of the Neanderthal genome published in 2010 revealed that we mated with Neanderthals in the Near East enough to share 1-4% of our DNA with them. On the heels of the draft sequence of the Neandertal genome, the same team published the Denisovan genome using DNA extracted from an exceptionally preserved finger bone from remains found in Denisova Cave in Siberia. The archaeological data at Denisova show a mixed toolkit with elements of Upper- and Middle-Paleolithic industries. Molar morphology indicated Denisovans were distinct from both modern and known archaic humans. The genomic data indicate Denisovans were indeed a new species with unique genomic markers. The power of modern genomics allows us to also find evidence of mating with modern humans, specifically modern Melanesians who share 4-6% of their genomes with Denisovans. Were these matings clandestine trysts or was there more at stake—some flow of genes to modern humans that helped us adapt to the novel environments of Europe and Asia?

Genomic breadcrumbs? Preliminary comparisons between Neandertal and human genes indicate significant differences in aspects of cognition, metabolism, and skeletal and skin morphology. But what about the inherited portion of the genome? Does it have a role in any functional aspect of our biology and physiology? Dr. Green, lead author on the draft sequence of the Neandertal genome described the inherited portion as ‘sparsely distributed across the genome, just a ‘bread crumbs’ clue of what happened in the past’. But two new papers tell a different story, suggesting that inter-breeding may have significantly contributed to successful adaptation to the new environments of Eurasia.

In the summer of 2011, another team identified a Neandertal origin for a unique cluster of co-inherited gene variants (a haplotype) in the non-coding segment of the dystrophin gene on the X-chromosome. This haplotype occurs at a frequency of 9% in all modern non-African human populations and likely first appeared in the genome prior to or very early in the migration out of Africa. The authors of the study posit that either this genetic (and/or cultural) exchange enabled successful modern human adaptations to the novel environments of Eurasia. There is an intriguing possibility that human males left Africa in greater numbers and mated with archaic females: an earlier study on modern human variation found the X-chromosome experienced more than expected genetic drift at the time of human migration out of Africa, a pattern not found in the migrations into East Asia and Europe.The authors of this study conclude that female effective population size was reduced compared to males due to some sex-biased process or natural selection affecting the X-chromosome in non-African populations.

Speculations that inherited genomic material conferred a fitness advantage gained further ground in a study published this summer in Nature. A Stanford University team identified HLA gene variants that are rare in modern Africans but significantly present in West Asians, again suggesting genetic admixture outside Africa prior to Eurasian expansion. HLA class I genes are critical to the immune system because they target and destroy pathogens. The authors of the study argue that inter-breeding restored HLA diversity that was reduced by a population bottleneck in migration out of Africa, citing examples of similar events in the evolutionary genetic history of the peopling of the Americas. Not only was diversity restored to modern humans but new immune variants specifically adapted to local pathogens may have been acquired in the process as well. HLA-A*11 (associated with Epstein-Barr virus protection), for example, has become a dominant form in non-African populations occurring at rates of 64% in East Asia and Oceania (and even more in Papua New Guinea) suggesting strong selection. The high frequency of these gene variants (as compared with other regions of the genome) may be explained by the need for the immune system to be flexible to new pathogens (particularly rapidly evolving viruses), rendering it more susceptible to the forces of natural selection.

The future of the past. If the data from these various studies is supported by future work, we may end up rethinking our relationship to our closest cousins – were we separate species? Even field biologists who have the array of genes, biology, physiology and behavior sometimes have trouble determining whether two groups be classed as separate species or not. For those working in paleoanthropology or paleogenomics, the dataset is even more limited and the creation of new taxa is temporary pending further data but useful as a heuristic tool.

The field of paleogenomics is relatively young and has a tremendous number of methodological and technical challenges to overcome before we can comfortably say that the sequences yielded are authentic and reliably represent the genetic data. A major challenge is verifying and authenticating the endogenous (or local) DNA in a specimen that has been potentially contaminated by microbes and human researchers. The past decade has been punctuated by marvelous advances that have helped us better understand recent human evolution and ourselves. The possibility that our advantage in global colonization derives from early acts of inter-breeding is a fascinating one. With the rapid advancements in technology and increased interest in ancient DNA, the future looks promising for unraveling the story of the immediate past.

1. Green, R. E. et al., Science 328, 710 (2010).
2. Reich, D. et al., Nature 468, 1053 (2010).

A lipid, the terpenoid camphor is found in Cinnamomum camphora, an Asian evergreen tree commonly called camphor laurel. Incidentally, the volatile eucalyptol is at a slightly higher concentration in extracts of camphor wood. Rosemary leaves have a large camphor component as did last week’s smell of the week (coriander). Camphor itself is used for it’s aromatic properties for cooking and incense but has medicinal uses as well, particularly as an antibiotic.

Like many herbs, coriander has potential health benefits, chiefly in its high levels of antioxidants in the leaves. Due to a high level of aldehydes and a potential genetic effect, some people don’t like coriander because it is perceived as soapy. Intercropped with tomatoes, coriander masks tomato odor volatiles that are attractive to the silverleaf white fly and reduces infestation with these pests.

At the chemical level, the main volatile in coriander seed is d-linalool. Linalools are terpene alcohols and commonly found in flowers and spices. It’s pleasant scent makes it a key ingredient in the decorative cosmetics  industry. Other important volatiles are pinenes (alpha and beta), diterpenes, p-cymeme, and decylaldehyde (the ‘soapy’ compound)–even a touch of camphor (perhaps a future smell of the week!). Coriander leaves (cilantro to some) have been less studied but are mainly saturated and unsaturated aldehydes 83%) and alcohols (17%).

While there are many cilantro (leaves, not the seeds) haters out there, some can be converted  I do detect the soapiness, especially if the leaves aren’t very fresh, but it doesn’t seem to bother me much. If not in a hurry, I tend to crush my cilantro with the knife edge, which apparently may reduce the aldehydes. Maybe I’ll conduct an experiment with crushing versus not-crushing. Either way, it’s hard to avoid in most cuisine and I am glad I am not a cilantro hater.