One Man’s Weed Is Another Man’s Science

When I was a teenager, my father would sooner believe that I was an incompetent lawn mower than even entertain the possibility that I was motivated to preserve what he considered weeds, those suburban symbols of lassitude and irresponsibility.


If I’d see a patch of flowering clover or the tiny star-like flowers of stitchwort (Stellaria),I felt compelled to mow around them, come back to the patches with lawn clippers to cut protruding blades of grass and try to make the weeds as inconspicuous as possible, hoping to sneak my conservation effort past my father’s critical eye.  But it never worked. Even though I tried to point out that stitchwort was rich in vitamin C, in his eyes there was a place for everything, and only grass should be grown in lawns.

I discovered that one of my father’s many kindred spirits lives on my street. A few nights ago while walking my dog, I noticed he was destroying an attractive patch of black medic from his lawn that bordered the sidewalk.

With the friendliest tone I could manage, I asked him, “Did you know that plant is a member of the legume family, and it makes its own fertilizer?”

“Yes, but it’s not nice,”  he replied.

I sensed it was hopeless, but my compulsion to explain science obliged me to continue. “The nitrogen from the air gets converted to useful ammonium by a helpful bacterium in that plant’s roots,” I said.

“Yes, but it’s not nice,”  he repeated, still friendly.

For the sake of neighborly relations, now seemed like a good time to let go, so I smiled and concluded, “Oh well…it’s your property.”

black medic

So, alas, unable to spark a street discussion of the intricacies of black medic, I turn once again to the laptop keyboard. Medicago lupilina, is a member of the pea family (Leguminosae or Fabaceae). A close look at the cluster of yellow flowers reveals a set of miniature pea-like flowers. The bases, sepals and stamens are fused together into a cup-like structure, and you have to lift the cup and have exceptional closeup eyesight to see its reproductive parts.

A key ecological feature of this family is the nitrogen-fixing ability shared by most of its 18 to 20 thousand members. It happens through a symbiotic association with Rhizobium, which infect legume roots and form nodules, where in exchange for sugars, the bacteria use an anaerobic reaction to convert diatomic nitrogen into ammonium ion (NH4+). In the reaction, the nitrogen is “fixed”, because plants cannot convert relatively inert N2 into needed amino acids, but ammonium will do the trick. But free nitrogen gas has an oxidation number of zero, and it gets converted into  NH4+ , whose nitrogen atom has an oxidation number of (-3). This reduction process would not occur if the common oxidizer in air, oxygen, would come into contact with the nitrogen-fixing enzymes.

root nodules of black medic

But the problem is that the natural form of nitrogen fixation has something in common with the industrial version (Haber Process): it is an energy-demanding reaction,and what better way is there to release energy from sugars than through cellular respiration, which needs oxygen?

The bacteria get around this dilemma by making use of leghemoglobin(LEG), a pigment similar in structure to our hemoglobin but with a higher affinity for oxygen. In the diagram, notice that the pigment is actually in the nodule, outside of the bacterial cell wall, away from the enzyme complex (NC).

Nfixing_1The small amount of oxygen is then delivered to the bacteria’s respiratory chain (RC), allowing several ATP molecules to be fed into the enzyme complex, where the reducing agent, NADH, converts the nitrogen into ammonium. The latter is released in aqueous form into the host cell , where it is converted into glutamine, asparagine and urea derivatives of the general form,R-CO-NH-CO NH2, where R can be a different hydrocarbon group.

These products are then transported to the rest of the plant through the xylem (not with sugars, which are distributed by the phloem), and with the abundance of these protein-building blocks, it is not surprising that the seeds of the black, ripe pods of black medic, like those of beans, lentils and other legumes, are rich in proteins.

seed of black medic in my hand

Compared to other plants, legumes seem to be more sensitive to increases in carbon dioxide levels.(Incidentally, we have surpassed the global average concentration of 400 ppm,and you could see how it varies globally here.) Some species produce bigger seeds when the atmosphere is CO2-enriched, and in general, at least in soybeans, extra carbon facilitates the fixation of nitrogen, provided that there are no other stresses such as limited nutrient availability or drought.

I guess that’s another reason why my neighbor was digging up his black medic—better get to it before climate change amplifies his problem.


Will Elevated Carbon Dioxide Concentration Amplify the Benefits of Nitrogen Fixation in Legumes?1
Plant Physiology November 2009 vol. 151 no. 3 1009-1016  (available in its entirety, free of charge)
The Botanical Garden Volume II: Perennials and Annuals. Roger Phillips and Martyn Rix. Firefly. 2002

Autumn Leaf Chemistry: More Than Just Eye Candy


The Etymology And Drugs Of Parsley

My first language is a rough southern Italian dialect, scorned by many Northerners. But what I like about my mother tongue is the connection between some of its vocabulary and Linnaean taxonomy.

Parsley for instance is known as  prezzemolo in standard Italian, but I grew up calling it petrosino. Interestingly parsley’s genus, derived from Latin, is Petroselinum. The modern Italian word also originates from Petroselinum, but obviously the dialect-version of parsley is closer to its roots, pardon the pun. The English word seems to have been influenced by the Old French peresiland by the old English petersilie, which in turn is an offshoot of the Latin.

The Greeks once referred to the herb as petroselinon, which meant “rock celery”, but the modern Greek word is based on the Turkish word maydanoz.

Petroselinum latifolium  photo by Forest and Kim Starr

Petroselinum latifolium; credit Forest&Kim Starr

Now that we know parsley’s etymology, we can investigate its chemistry. Simple distillation equipment may be fine for creating moonshine, but it will not do much to separate the compounds of parsley or of any plant for that matter. What’s needed is the Likens Nickerson Method. The parsley-water mixture is placed in one flask, and a separate flask holds an organic solvent. Both are boiled while being connected to a shared set of columns and condenser. Using dry ice, water is removed from the fractions, and eventually the compounds are separated and identified through good-old gas chromatography-mass spectrometry.

The main volatile component of oils in parsley is apiole (also spelled apiol), C12H14O4 .

All sorts of medicinal properties have been attributed to apiole since the mid-19th century, but in concentrated form it can do a number on your kidneys and liver.
The apiole molecule bears a strong resemblance to another substance found in small quantities in parsley: myristicin.

Myristicin is the notorious alkaloid drug which is also found in nutmeg. In the latter, it is found in a greater percentage and coexists with other natural drugs. In the 1970’s pursuit of altered states inspired many inmates to ingest spoonfuls of the spice. Possible side-reactions include chemotherapy-like vomiting and possibly death, a somewhat high price for hallucinations.

As we compare the structure of parsley’s non-psychoactive apiole to that of myristicin, we notice that one of the methoxy(O-CH3)groups is also replaced with hydrogen.

As is often pointed out in the literature, myrisiticin, although not an alkaloid, is structurally very similar to peyote’s hallucinogen, mescaline. Rather than being part of separate methoxy groups, the oxygens in myristicin form a heterocyclic ring, and in mescaline, the allylic group is in a reduced state and the tail-end carbon is replaced with an amino group.

The similarities in natural products are not coincidences. In their bio-synthesis, they share a common pathway. Side-reactions then occur for various reasons, and they are subject to natural selection.

Molecules, like words, often have common roots, but they are in a constant state of flux.


  • The Merck Index. Twelfth Edition
  • Pol. J. Food Nutr. Sci. 2005, Vol. 14/55,No 1, pp. 63–66

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