Tag Archives: anatomy

The adoration of the pine nut

It’s the winter holiday season, when halls are bedecked with garlands of evergreens, sprigs of holly, and bunches of mistletoe to remind us that there is life in the darkness and love to be shared. This year, Katherine has added another symbolic plant to her own holiday list – pine nuts. They are more precious this year than ever.

I first started using pine nuts in holiday baking for the simple reason that they taste like pine and thus add a Christmas-tree note that almonds do not. A deeper significance was not on my mind. But pine nuts are so interesting botanically that I always slice some of them open to look for tiny pine embryos inside, and that triggers some nostalgia for conifer week in the botany lab I taught as a graduate student (along with the best co-TA ever). Specifically, I think about an odd conversation with one of the students, which for years was nothing but another funny story. Only now, decades later, do I understand that this student’s observations have something to teach us about the true meaning of pine nuts.

The remarkably unfiltered conversation happened after our student, while dissecting a pine nut, had experienced a double epiphany: he finally understood the details of sexual reproduction in pines, and he therein discovered a pathetically apt metaphor for his love life. I can still see the way he dropped his shoulders as dejection slid across his face. His exact words are lost after so many years, but he basically confided to us that, like a pine seed, he always invested a little too much and a little too early in the promise of love (or at least sex) which might never be fulfilled.

Lessons from pine sex

Both pines and flowering plants make seeds, however they don’t feed their embryos the same way. Pines (and other gymnosperms) pack a fat lunch in anticipation of an embryo, whereas flowering plants typically wait for successful fertilization and only then build up a food reserve for the embryo. Pines invest in an uncertain future, while flowering plants hold back and hedge their bets. Our student thought that his was a losing strategy, and that he should behave more like a flowering plant, but I’m not sure. I like to imagine that someone found his earnest vulnerability charming, and that he has found the loving partnership he was looking for. No matter what happened in his case, however, this I now know for certain: sometimes in life you have to muster the courage to invest fully, even recklessly, in hope. I think that’s a pretty good message for the short days of winter.

The full story of pine reproduction starts with the story of seeds, which is very complicated and still not fully resolved, but here it is in a nutshell. Seeds were an incredibly successful evolutionary innovation because they took a process that depended on wet soil or water pooling on bark or in sidewalk cracks and brought it inside a protective shell that remained on the parent plant and could function without free water. The ancestors of seed plants were similar to today’s ferns, in that they shed spores that germinated in moisture and grew into tiny plants that made eggs and swimming sperm. There are variations on this basic system throughout the plant kingdom, but ferns are a familiar example. In ferns, the large frondy generation is called the sporophyte (“spore plant”) because it makes spores. (Spores result from meiosis, so they contain half as many chromosomes per cell as the sporophyte does). Spores germinate and grow into flat green plants about the size of a lentil. These are called gametophytes because they make gametes (eggs and sperm). Under the right conditions, eggs and sperm meet, and the result is a new sporophyte.

A flat-topped Italian Stone Pine (Pinus pinea) on the Stanford campus
The tree in the center is a flat-topped Italian Stone Pine (Pinus pinea) on the Stanford campus

Pine trees are also sporophytes, but they hold onto their female spores, which develop into egg-producing female gametophytes* inside the seeds on the scales of their cones. The male spores are shed as pollen grains, with sperm-producing cells inside. Whereas free-swimming fern sperm cells get nowhere without a film of water between themselves and some eggs, pine sperm packaged into pollen grains can float through the air towards more distant eggs. Although non-seed plants have done well evolutionarily – mosses and ferns are especially diverse, widespread, and abundant – the seed habit has freed gymnosperms and angiosperms from some ecological constraints and has undoubtedly contributed to their success in a range of habitats.

What is a pine nut?

For all its oily goodness, botanically a pine nut is not a nut at all. It is a seed, and without its shell (the seed coat), a pine nut is essentially nothing but female gametophyte, often with a cute little embryo inside bearing tiny pine needles. Long before it gets to that point, however, the gametophyte has to do what its name calls for – it makes eggs, two of them – and it also accumulates a lot of nutrients for a potential embryo. A typical commercial pine nut is about two-thirds fat by weight and one-third protein and carbohydrates. A tree invests in making hundreds or thousands of those energy-rich structures each season, even though only some of the eggs will be fertilized. I don’t know what proportion of the ovules (immature seeds) are actually fertilized on a typical tree, but in a bag of pine nuts it is sometimes hard to find any with an embryo inside. Other times, most of the seeds I open up do contain baby pines.

Pine nuts are worth dissecting in your kitchen because they give you a rare glimpse into the evolutionary history outlined above. By contrast, you will never see the female gametophyte of a walnut, pecan, almond, hazelnut, peanut, or cashew, at least not in your kitchen. In flowering plants, the female gametophyte has evolved to be just a handful of cells, and when we eat an angiosperm seed, we are eating some combination of embryo and that special made-just-in-time tissue called the endosperm.

Conifer week in your kitchen

Just for auld lang syne, I gathered and photographed some of the materials we might have used during conifer week in botany lab so that you can follow along at home. If you have your own pine nuts, that’s even better. Epiphanies are encouraged but not required.

Commercial pine nuts are harvested from natural stands of a few large-seeded species. European pine nuts come from the Italian stone pine, Pinus pinea, which is planted as an ornamental in other Mediterranean type climates, including, fortunately, the campus of Stanford University where I teach. Squirrels are also a conspicuous part of the flora and fauna at Stanford, and they had already taken most of the seeds out of the cones that I picked up. In fact, pine nut processors usually harvest cones directly from the tree before their scales have opened up, and the cones are allowed to dry at a safe distance from seed predators. Unfortunately, the remaining seeds I found, stuck inside their cones and spurned by the squirrels, had become moldy, so all the photos here of gametophytes and embryos are from pine nuts I bought. Those were harvested in China and came from a different species, the Korean pine (Pinus koraiensis).

Seed poking out from between cone scales

For most of their development – between pollination and seed release – pine cones keep their scales tightly closed. You can usually find cones in various stages of development on a tree because the whole process can take two or three years. When seeds are mature, the scales of most species open up, and the seeds can be seen peeking out from between them. 

In pine species with small seeds, there is a prominent wing on each seed, and seeds flutter out away from the parent plant. Italian stone pines have very large seeds whose useless vestigial wings detach from the seeds easily.

The “shell” of a pine nut is nothing but a hard thick seed coat, its only protection against the outside world. This is what it means to be a gymnosperm — a naked seed. By contrast, the shells of other “nuts,” like pecans, almonds, or pistachios are part of the angiosperm fruit wall that surrounds the seeds, and their seed coats are very thin.

Most pine nuts are sold as bare gametophytes, without their seed coats. If you look at their pointed tips you can see a small opening where the pollen grains would have settled in to germinate and send out their pollen tubes. Pine gametophytes make two eggs in special chambers (archegonia), but usually the first egg to be fertilized is the only one that ultimately develops. I have never found twin embryos inside a pine nut, but it does happen. Twinning can also result when one embryo splits lengthwise early in development.

If you have any pine nuts to dissect, it’s best to use a razor blade because kitchen knife blades are a little too thick to do the job without mangling the embryo. A longitudinal section starting at the pointed tip reveals the embryo inside.

Above: row of pine gametophytes with embryos; below: embryos removed from the gametophytes

Here’s where it gets really interesting. Recall that one of the main functions of the female gametophyte, besides making the eggs, is to nourish the embryo. In other words, once the embryo starts to grow, it basically eats the gametophyte. It does this with the help of the suspensor, a column of disposable embryonic cells that push the main part of the new plant forward, into the gametophyte, so that it can absorb its nutrients. Once the embryo has established a distinct leafy end and root end, the root starts to grow back towards the suspensor and it crushes it. You can usually find the stringy dried up suspensor in the mature pine nut.

One of the things that makes pine nut embryos so adorable is the set of tiny needle leaves at their tips. When the embryo becomes a seedling, these will emerge to photosynthesize and take over the job of feeding the young plant. 

Pine nuts at Christmas

Italian stone pines (Pinus pinea) are native to the European side of the Mediterranean coast. In Italy they occur on the northern half of both sides of the peninsula and in the heel of the boot. The range continues westward along the southern coast of France and into Spain and Portugal where native stands are scattered throughout the interior (Viñas et al., 2016). Pine nuts were never domesticated and are generally not even cultivated in orchards. They are usually harvested from natural stands, as they have been for tens of thousands of years in Southern Europe. There is even evidence from a Spanish cave that Neanderthals collected and presumably ate P. pinea seeds (Finlayson et al., 2006). Modern humans kept up the practice and many traditional foods from the region feature pine nuts.

Pine nuts have a distinctive conifer flavor dominated by pinene, limonene, hexanal, camphene, and careen (McGee, 2020), and they work well in both savory and sweet dishes where they hold their own against strong herbs and spices. There is of course pesto from Genoa in the heart of pine nut country, but also Italian cakes (pinolata) and Christmas cookies (pignoli). A specialty in parts of Provence is the sweet tarte aux pignons . In Catalonia, All Saints Day (November 1) is celebrated with pine nut confections called panellets. None of these traditional recipes includes chocolate — likely because they predate its arrival into Europe — but I really like to bake with a combination of chocolate, orange, and pine nuts, especially at Christmas.

Puff pastry tart with leeks, bleu cheese, arugula, and pine nuts

Investing in pine nuts

For a pine tree, the substantial energy allocated to female gametophytes is an investment in potential offspring with no guarantee of success. For us, it can be a substantial financial investment that may be increasingly costly for people and the planet as well. Pine nuts have always been more expensive than peanuts or almonds, but their price jumped this year for a variety of reasons (Produce Report). Most pine nuts for sale in the United States come from stands of Korean pine growing in China. There, as everywhere, pine nut processing is unusually labor intensive and even dangerous, as rough heavy cones must be harvested by hand by skilled pickers who can navigate among the branches high above the ground. Seeds are then separated from the awkwardly knobby cones and the seed coats are removed from the female gametophytes. Pandemic-related safety measures and labor shortages have limited production, and the supply chain has been throttled, driving prices even higher. Meanwhile, a warming climate and a damaging insect pest have reduced yields (El Khoury et al., 2021). I’ll confess that I balked at the cost and used local pistachios in place of pine nuts in much of my baking this year.

The more I read about pine nut production the more concerned I became about worker protections and whether pine nut harvesting in natural stands could be sustained in the face of rising global demand. A conservation biologist working in Korean pine forests in Russia has written movingly about these highly diverse and fragile ecosystems, home to rare Amur tigers and other animals, and called for protections (Slaght, 2015).

Since a few western North American species produce large edible seeds, I looked for local harvesters who intentionally support both human and ecological communities. There are at least a couple of them, but neither had any product to sell this year. The future doesn’t look good for these businesses either, given the west’s megadrought and competition from lower-cost Chinese producers. Theirs is an investment against the odds and in favor of conserving an important cultural and ecological heritage.

The message of the pine nut

Besides their piney flavor and rich texture, what can we take from the precious little naked gametophytes that are now on my list of holiday plants? What message do I send to friends and colleagues along with my chocolate orange pine nut cake?

Pines have been around for about 150 million years, and conifers for twice that long (Rothwell et al., 2012, Jin et al., 2021), so their reproductive strategy can’t be that foolish. Their lineage persisted even when an asteroid slammed into our planet, causing the fifth mass extinction. If they don’t survive the Anthropocene, it won’t be because of their sex life. If anything, we should take their lesson to heart now more than ever. We can’t afford to wait until the last minute, like angiosperms do, to invest in future generations. It is time — past time, actually — to muster the courage and the will to dedicate all the resources we can to the preservation of the planet and our place in it. Otherwise, what hope do we have?

*note: Female gametophytes are more accurately called megagametophytes, and they derive from megaspores produced in megasporangia. Male gametophytes are really microgametophytes, pollen grains are microspores, and they are shed from microsporangia. In flowering plants, microsporangia are inside the anthers.

References and further reading

von Arnold, S., Clapham, D., & Abrahamsson, M. (2019). Embryology in conifers. Advances in Botanical Research, 89, 157-184.

El Khoury, Y., Noujeim, E., Bubici, G., Tarasco, E., Al Khoury, C., & Nemer, N. (2021). Potential Factors behind the Decline of Pinus pinea Nut Production in Mediterranean Pine Forests. Forests, 12(9), 1167.

Finlayson, C., Pacheco, F. G., Rodríguez-Vidal, J., Fa, D. A., López, J. M. G., Pérez, A. S., … & Sakamoto, T. (2006). Late survival of Neanderthals at the southernmost extreme of Europe. Nature, 443(7113), 850-853

Jin, W. T., Gernandt, D. S., Wehenkel, C., Xia, X. M., Wei, X. X., & Wang, X. Q. (2021). Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines. Proceedings of the National Academy of Sciences, 118(20).

McGee, H. (2020). Nose dive: A field guide to the world’s smells. New York, NY: Penguin Press.

Meade, L. E., Plackett, A. R., & Hilton, J. (2021). Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed‐bearing structures. New Phytologist, 229(3), 1782-1794.

Pine Nut prices reach record high. Produce Report. (2022, April 5). Retrieved December 15, 2021, from https://www.producereport.com/article/pine-nut-prices-reach-record-high

Rothwell, G. W., Mapes, G., Stockey, R. A., & Hilton, J. (2012). The seed cone Eathiestrobus gen. nov.: fossil evidence for a Jurassic origin of Pinaceae. American Journal of Botany, 99(4), 708-720.

Rudall, P. J. (2021). Evolution and patterning of the ovule in seed plants. Biological Reviews, 96(3), 943-960.

Slaght, J. C. (2015, October 19). Opinion | Making Pesto? Hold the Pine Nuts. The New York Times. https://www.nytimes.com/2015/10/19/opinion/making-pesto-hold-the-pine-nuts.html

Viñas, R. A., Caudullo, G., Oliveira, S., & de Rigo, D. (2016). Pinus pinea in Europe: distribution, habitat, usage and threats. European Atlas of Forest Tree Species; European Commission: Brussels, Belgium, 204.

The Botanist in the Root Cellar

How much actual root is in “root vegetables”?

The wintertime pantry is a study in vegetable dormancy. Our shelves brim with structures plants use to store their own provisions. Each embryonic plant in a seed—the next generation of oats, quinoa, dry beans, walnuts—rests in the concentrated nutritive tissue gifted to it by its parent. The starchy flesh within the impervious shell of a winter squash is alive, as are apples, hopeful vessels of seed dispersal. Maple and birch syrup are stored energy made liquid and bottled. And then there are the so-called “root vegetables.” The term covers a surprisingly anatomically varied set of nutrient storage structures, only some of which are actual roots. Our familiar root vegetables represent only a sliver of global plant species diversity but nonetheless include the majority of contrivances herbaceous plants use in order to live to sprout another season: taproots, hypocotyls, stem tubers, root tubers, corms, and rhizomes. Raiding your root cellar for the ingredients for a roasted root vegetable medley, then, provides a great opportunity to turn your dinner prep into a botany lab. All you need is a knife and cutting board.

Roasted stacks of sweet potato and parsnip, painted with sage butter and roasted. See Katherine’s sweet potato post for the recipe.

The case for tree thinking

First we need to consider the taxonomy of our candidate botanical subjects. Taxonomy is the scientific practice of grouping related organisms in hierarchies of similarity. We shove the continuous variation of living things into discrete boxes labeled species, genus, family, order, and so on. Carl Linnaeus started the taxonomic naming system two hundred years before Watson and Crick identified the double helix shape of deoxyribonucleic acid (DNA), marking the beginning of the genomics era. Modern practitioners bring many types of data—geography, fossils, genetics, morphology–to bear toward the twin goals of illuminating the pattern of plant species evolution and defining groups based on common ancestry.

A phylogenetic tree of the major plant clades. Each branch point (node) represents the common ancestor of the organisms on the descendant branches. A single food plant species is shown here at the tip of each branch, a sort of mascot for its lineage.

The visual embodiment of this effort is the tree of life (cladogram) that represents the pattern of plant species evolution by common descent (phylogeny–see our primer on reading phylogenetic trees and using them to understand broad patterns in plant evolution). Each branching point on the tree is a node that represents a common ancestor of all the descendant taxa on the branches that come from it. The species are like the leaves on the tips of the branches. A schematic tree of life is the only illustration in Charles Darwin’s On the Origin of Species, the landmark book that provided the kernels of the core theories of evolutionary biology. Modern scientific convention tries to match old taxonomic names—because they are familiar and useful as a practical matter–with nodes on the tree of life. Small branches connect species to genus. Larger branches connect genera to families, families to order. The deep internal named nodes show the origin of the major clades. A clade is a group of organisms that descend from a common ancestor. A major clade is a significant branch on the plant tree of life that scientists have named for convenience of reference. You may remember some of these from biology class, like “monocot” and “dicot.” The former (monocots) has held up as a robust clade, but dicot is more complicated.

Green garlic, a monocot that stores its winter provisions as a bulb

As it happens, plant taxonomy before the advent of genetic data was reasonably accurate.  Even though our understanding of plant species evolution is far from complete, genomic analysis has provided few big surprises about common ancestry of plant species and membership of taxonomic groups. Early taxonomists had the wisdom to rely primarily on similarity of reproductive structures—seeds, fruit, flowers, spores, cones—to circumscribe named groups. Reproductive structures tend to change more slowly over evolutionary time than do vegetative structures in plants. So one may expect to find a fair amount of coincident similarity among distantly related species in roots, shoots, and leaves.

This is where our categorization of root vegetables by taxonomy collides with our categorization of them by morphology. In short order we will organize our root vegetable species according to which structures the plant has chosen to amplify as a subterranean or soil-adjacent storage organ. This is not the same pattern as taxonomic organization. Grouping our root vegetables by taxonomy first helps us understand similarity and difference within and between groups of closely related plants—families, in this case. In doing so we can develop gestalt for the culinary qualities within plant families and appreciation for the evolution of plant diversity evident on our own dinner tables.  Consider this intellectual nourishment, or perhaps the advent of a lens with which to view familiar foods anew.

Placing root vegetables on the plant tree of life

Around the globe humans utilize many dozens of plant species that bear underground (or near enough) storage structures. The most recent generations of people overwintering in the United States or Europe, however, chiefly engage with only a few. Perhaps only the most dedicated winter vegetable enthusiast will be familiar with all of the species on the following roster of root vegetables potentially available in Western grocery stores or farmer’s markets, although the list is unlikely to be exhaustive. I have organized the root vegetable species by families, and the families by major clade. Our list includes 15 of the 446 currently recognized plant families.

Whole sweet potatoes (Convolvulaceae)–NOT yams (Dioscoreaceae), NOT potatoes (Solanaceae), and NOT oca (Oxalidaceae)

Please take note of the disambiguation about the words “yam” and “potato.” The tubers marketed as “yams” in most American groceries are mostly actually sweet potatoes, which are also not potatoes. True yams are large tubers that are staples of tropical diets but relatively scarce in northern diets or groceries. In New Zealand the Andean oca is also known as “yam.” All of these are in different plant families.


  • Amaryllis family (Amaryllidaceae): onions and shallots (Allium cepa), garlic (Allium sativum), leeks (Allium ampeloprasum), and other alliums
  • Ginger family (Zingiberaceae): ginger (Zingiber officinale), turmeric (Cucurma longa)
  • Dioscoreaceae: true yams (several species in the genus Dioscorea), including the purple yam (ube; D. alata).
  • Sedge family (Cyperaceae): water chestnut (Eleocharis dulcis)
  • Arum family (Araceae): taro (Colocasia esculenta)

Eudicots: asterids

  • Goosefoot family (Amaranthaceae): beets (Beta vulgaris)
  • Sunflower family (Asteraceae): salsify (Tragopogon porrifolius), burdock root (Arctium lappa), sunchokes (Helianthus tuberosus)
  • Carrot family (Apiaceae): carrots (Daucus carrota), parsnips (Pastinaca sativa), parsley root (Petroselinum crispum), celery root (Apium graveolens)
  • Morning glory family (Convolvulaceae): sweet potatoes (Ipomoea batatas; often mistakenly called “yams” in the United States)
  • Nightshade family (Solanaceae): potatoes (Solanum tuberosum)

Eudicots: rosids

  • Spurge family (Euphorbiaceae): cassava (manioc, yucca; Manihot esculenta), the source of tapioca
  • Mustard family (Brassicaceae): turnips (Brassica rapa), rutabagas (Brassica napus), kohlrabi (Brassica oleracea), radishes (genus Raphanus), horseradish (Amoracia rusticana), wasabi (Eutrema japonicum), maca (Lepidium meyenii)
  • Nasturtium family (Tropaeolaceae): mashua (Tropaeolum tuberosum)
  • Legume family (Fabaceae): jicama (Pachyrhizus erosus)
  • Oxalis family (Oxalidaceae): oca (Oxalis tuberosa), an Andean vegetable that is confusingly called “yam” in New Zealand

True taproots: carrot, parsnip, parsley root, salsify, burdock root, horseradish

Carrots (taproot and leaves–which make a great pesto)

Now grab a carrot, parsnip, parsley root, salsify, or burdock root for your roast vegetable medley. These are the only true taproots on our list. The roots are much longer than they are wide and taper to a point. Thin lateral roots sprout from them in random locations or in discrete vertical lines. If you cut it open and examine it in cross section you see the tough core of xylem-rich pith (water conducting tissue) in the middle surrounded by a cortical layer that separates the pith from the sweet storage tissue (parenchyma) and sugar-moving phloem that surrounds it. You have likely removed the aboveground greenery from these plants but should be able to tell or recall that it appears as if the leaves grow directly out of the crown of the taproots. They almost do. The anatomical stem on carrots and parsnips is a highly reduced disk on top of the taproot that serves as a bud-studded vascular transfer station, shuttling water and nutrients from the taproot into the leaves and flowering shoots.

Horseradish is also a taproot. A little bit grated into a sauce would make a delicious accompaniment to your roast vegetable medley. Incidentally, horseradish powder is the main ingredient in cheaper “wasabi” products available in American grocery stores, as the horseradish taste is superficially similar to that of true wasabi, which is also in the mustard family. Wasabi is also a root vegetable, but its underground storage structure is a rhizome, an underground stem, not a taproot.

Roots fused with stems (hypocotyls): celery root, beet, rutabaga, turnip, radish

celery root hypocotyls

A hypocotyl is a swollen fusion of taproot and stem base. The taproot portion is covered in fibrous secondary roots, most spectacularly in celery root. Leaf scars will be visible about these lateral roots, either surrounding the entire upper portions of the hypocotyl, as in celery root, or just at the top, as in beets and the mustard family hypocotyl vegetables (turnip, rutabaga, radish). All hypocotyl vegetables aside from beets are structurally straightforward but different from the taproots. A single layer of vascular tissue lays below the skin surface and penetrates into the storage tissue.

A rutabaga hypocotyl in the ground

Beets, however, are built from concentric rings of vascular tissue (xylem and phloem) and storage tissue (parenchyma), which is visible when the beet is cut in cross section. This ring structure is unique to the taxonomic order Caryopyllales, of which beets are a member. And as Katherine notes in her excellent beet post, the vibrant colors and earthy smell of beets are also unique. The former is due to betalain pigments, which are also unique to the Caryophyllales and distinct from the anthocyanin pigments present in all the other vegetables in our list (see our pigments post for a quick rundown of the most common pigments). The earthy smell is from a compound called geosmin. Beet is the only plant known to make it, and nobody knows why. Geosmin us usually produced by microbes in the soil and is liberated after rain to create that marvelous fresh smell after a storm.

chiogga beets show concentric vascular rings in dramatic fashion

Indidentally, our hypocotyl root vegetables here are all varieties, or subspecies, of species that also produce familiar leafy vegetables: rutabagas and the Russian or Siberian kales; turnips and Napa cabbages and mizuna; beets and Swiss chard; celery root and celery stalks or seeds. In each of these cases the variety produced for leaves has a much less pronounced hypocotyl than the variety produced as a root vegetable. Similarly, while the leaves on our hypocotyl root vegetables are all edible, they will be smaller and tougher than those on the varieties that have been bred for leaves. 

Bulbs: onion, garlic, shallots, leek

red onion bulbs growing in a planter box

Onions, shallots, garlic and other alliums might be the most famous “root vegetables” of all, but their delicious parts are constructed entirely of swollen modified leaves. The papery tunicate covering surrounding the fleshy leaf bases are also constructed out of modified leaves, all arising from the basal plate (true compressed stem) that interfaces with the spindly roots on the bottom. The fleshy part of each garlic clove is a single fat modified leaf. Inside each garlic clove or onion bulb is an apical bud that will send up new leaves and flowering shoots. Everyone who has had onions and garlic sprout on them can observe this. You can of course plant these sprouting bulbs in the soil to make a new plant. A leek is a bit intermediate between a true bulb and a big herb. They call the lower white region of overlapping succulent leaf bases a “pseudobulb,” a nod to the messy continuous nature of biology and the difficulty with labels.

slices of leek pseudobulb, showing overlapping leaf bases

Unless you’re using a variety of “sweet” onion, which has been grown or bred to lack sulfurous aromatic compounds, you might tear up when you’re cutting onions and shallots. Cutting these bulbs volatilizes the irritating compounds that otherwise protect our favorite bulbs from pests.

Root tubers: sweet potatoes, cassava

A root tuber is an enlarged root that stores starch and other nutrients. Smaller lateral roots often branch from its surface and obtain water and soil nutrients. Raw sweet potatoes are readily available candidate root tuber ingredients for your botanical scrutiny and roast vegetable medley. Cassava is not, nor should it be, at least in root tuber form. Starch derived from cassava might be elsewhere in your pantry as tapioca.

A convenient aspect of our most commonly used root vegetables is that they require very little manipulation or preparation before they can be consumed. You don’t even have to peel your sweet potatoes before you cook them. Raw cassava tubers, however, are laced full to bursting with cyanide. They are the third most important source of calories throughout the tropics, behind corn and rice, but require extensive preparation before consumption to remove the cyanide, including grating, drying, leaching and cooking.

Cassava tubers develop underground from certain roots that become fleshy storage structures. They continue to acquire water and nutrients via smaller secondary roots that dot their surface. If the plant in question grows from a seed, then the harvestable storage root may develop from the taproot that grows from the seed. This, however, proves an inefficient way to farm these species, as many more storage roots can develop on a single plant when that plant is started from a shoot—a stem with leaves. This is where the visual heuristic of placing root vegetable species on the branches of the plant tree of life gets literal with sweet potatoes and cassava. The key factor is the presence of numerous nodes—leaves along the stem and their attendant axillary buds. Cassava and sweet potato are among the plant species that can generate roots from the buds in their leaf axils under the right conditions, namely being in contact with moist soil. Roots that develop from non-root tissue (like stems) are called adventitious roots. When several nodes of a shoot are planted in the soil, many adventitious roots will develop, of which some can become enlarged storage roots. In cassava the starting shoot is a cutting from a mature cassava plant. In sweet potatoes the starting shoot is called a slip. Slips grow from buds on the proximal (closest to the parent plant) end of sweet potato tubers. On sweet potatoes this is the end with the scar where the tuber was cut away from the parent plant.

sweet potato developing slips

Rhizomes: turmeric, ginger, galangal, lotus, arrowroot, wasabi

A rhizome is a fleshy underground stem. It grows horizontally and sprouts new plants. Stems grow upward from buds near the soil surface, and roots grow from buds on the underside of the rhizome. It is structurally similar to stem tubers, like potatoes (see below), but it only grows horizontally, not in any direction, like a tuber. Rhubarb, asparagus, and irises also spread by rhizomes. If you decide to get out ginger or turmeric to flavor your vegetable medley, you’ll notice structural similarities to stem tubers, including nodes with buds.

Stem tubers: potato, sunchoke, jicama, yam

The eyes may or may not be the window into the soul, but they are our most conspicuous clue that potatoes are subterranean stem tubers, not roots. Katherine’s superb post on potato anatomy will walk you through this (potato) eye exam. Observe both ends of a potato. One end (the proximal end) bears the stump of the stolon (horizontal stem) that connected it to its mother plant. The other is tightly packed with small eyes that spiral out and around the potato. This is the growing (distal) end of the potato. New eyes originate at this end, so each eye is progressively older as you move toward the middle of the potato. Each eye contains a cluster of buds subtended by a semicircular leaf scar. The leaf in question was vestigial, translucent, and a remnant of it may still be present on your potato. Eyes are most easily visible on the “waxy” potato varieties (like Yukon Golds), which have less starch overall and a different ratio of types of starch than the “starchy” varieties (like Russets)–see Katherine’s post on potato starchiness for details.

potato eyes in spiral arrangement

The buds in each eye are axillary buds, structurally the same as Brussels sprouts. If your potato is exposed to enough light or warmth, the axillary buds will grow into new leafy stems, each of which can create a new potato plant. In this case your potato might also start synthesizing chlorophyll, turning it green. It will make toxic compounds at the same time, though, so if your potato is green you should either liberally peel it or wait to plant it in the spring.

Brussels sprouts on the stalk with residual leaf petioles. Brussels sprouts are spectacular axillary buds.

Nodes and buds are also easily visible on sunchokes, less so on jicama. True yams are actually structurally intermediate between rhizomes and stem tubers in that they might sprout adventitious roots. If you get your hands on an actual yam, instead of a sweet potato, you might see these.


Corms: taro, water chestnut (with a note on kohlrabi, which is not a corm)

A corm is yet another method by which plants have modified their stems to store starches and nutrients underground. The storage tissue is a swollen area of the stem above the roots and below the apical bud, from which leaves and flowers develop. Lateral buds on the stem produce modified leaves that produce a protective tunicate sheath around the starchy corm tissue. A thickened basal plate on the bottom interfaces with the roots and may sprout new corms (cormels). If you get canned water chestnuts or taro corms for your vegetable medley, these structures should be visible to you. Structurally, a taro corm is most similar to kohlrabi, which is what happened when plant breeders long ago took a weedy ancestral cabbage plant (Brassica oleracea) and bred for fat, bulbous stems. The leaf scars out the outside of a kohlrabi, and the nubbin of a root on the bottom, reveals that it is entirely stem.


The geophyte lifestyle

Potatoes are in the same genus (Solanum) as tomatoes (S. lycopersicum) and eggplants (S. melongena). The potato is the only one of these close relatives that hails from high in the Andes, where its underground tubers store the starches it needs to survive the harsh alpine conditions. This is a common ecological theme. Plants that create underground storage organs to withstand winter or seasons of drought are called geophytes. Even our short list of root vegetable species demonstrates that the geophyte lifestyle independently pops up all over the plant evolutionary tree, presumably in times and places where it may be adaptive. Even in just the Andes alone, potatoes are not the only domesticated geophyte crop with lowland relatives in the same genus devoid of starchy storage organs. Oca, confusingly called “yam” in New Zealand, where it was introduced in the mid-19th century, is otherwise known as Oxalis tuberosa. It makes stem tubers, like a potato. The specific epithet “tuberosa” separates it from non-geophyte species of Oxalis that are probably familiar to hikers and gardeners throughout the northern hemisphere. American health food stores sell dried maca hypocotyl (Lepidium meyenii) as a health food supplement, even though it is a staple crop throughout montane South America. Other Lepidium species are weedy little mustard plants. In the summer your garden may be teeming with flowering nasturtiums (Tropaeolum majus). You’ll notice a distinct lack of a fat, starchy stem tuber. Not so with mashua (Tropaeolum tuberosum).

branched taproot on a carrot

You should be well on your way at this point to getting your root vegetable medley into the oven. Finish peeling your vegetables, if you must, and dice them into approximately equally sized chunks. Toss them with a small amount of oil and salt. Add herbs if you would like. Spread them in a single layer on a baking tray or roasting pan and roast in the oven at 375 degrees Fahrenheit until they are tender, about 40 minutes. It is helpful to turn the pieces and move them around with a metal spatula halfway through the cooking time.

I like to serve these roast vegetables with some kind of sauce, often a strained yogurt mixed with salt and herbs. This is a dish filled by design with concentrated energy to maintain life through harsh seasons. The geophyte lifestyle is periodically useful for us all.

The Botanist Stuck in the Kitchen With You (and Peas)

I am about to start an 8th week of online teaching and my county’s 11th week of sheltering in place. While the (essential and life saving) sheltering is getting really old, the academic quarter has sped by as usual, along with its relentless parade of deadlines and grading. Our current crisis may have no definite end, but the academic quarter must wrap up on time, ready or not.

Some people are reporting really vivid dreams right now, however, for me, the most noticeable side effect of working and teaching from home is that I never stop thinking about it. Like midway through a Saturday night screening of Reservoir Dogs when I was suddenly reminded of peas and the upcoming class meeting on fruit. Can I do this online? We’ll just have to see, won’t we?

Oh, and don’t be a Mr. Pink.

Apologies to Stealers Wheel, the terrific Michael Madsen, and his PSA on sheltering.


Closeup of sugar snap pea flower with tiny developing fruit.

The Botanist Stuck in the Kitchen, rummaging for beets

Over these many weeks, humans have been forced into an uncomfortably close study of our own species’ behavior. Observations haltingly stream in through the internet and the TV, through hurried forays into the sparse public square, and through sometimes painful introspection. We are finding what we’ve always known, that humans are petty and petulant, compulsively social, and surprisingly sublime.

Meanwhile, without our clueless interference, non-human animals have gone about their business as normal. The male bi-colored redwing blackbirds where I live are putting on the biggest and flashiest red patches I’ve seen in years. Good luck, guys!

And the Canada geese, which normally annoy me with their poop and their nasty moods have become adorable as they sashay in pairs down the road towards their new nests on the empty golf course. In a few weeks they will be justifiably nasty again, hissing as they protect their babies from me, a silly runner, just trying to shed my own cranky mood into their territory.

Recently, after a run through a muddy patch of the trail stamped with goose footprints and lined with wild sea beets, I remembered that I had some old beets in the refrigerator. Time to do some botany!

For much more information about beets and their relatives, see our longer posts.

Sheltering in the kitchen with oatmeal

My first week of trying to teach remotely has wrapped up, and I finally found a quiet moment to record another video from my kitchen. That moment was 5:45 am.

Most of the US has already spent weeks sheltering at home, and people are getting creative and socially expressive. Thus, apparently, I am already late to the oatmeal video trend. True, oatmeal is exactly the sort of food we need right now. It’s comforting, affordable, nutritious, easy to make, and ripe for virtue signaling. No wonder people want to share. But really, do any of those other videos give you three botany lessons in under 6 minutes? I didn’t think so.

So…am I a morning person? Yes indeed. Have I been rewatching my favorite Tarantino movies? Yes, yes, I have. He has a thing for breakfast cereal. And bathrobes.

Now – if any of you have any more questions, now’s the time. Or you could just check out our more detailed posts about pecans and walnuts.

The Beet Goes On

In this Valentine’s Day edition, Katherine brings you a love song with a beet. Sweet and red, sort of heart-shaped, bearing rings, and definitely divisive – beets should be the unofficial vegetable of the holiday. And if you don’t feel like celebrating, then you can just sit alone and eat dirt.

Throughout two years of dating and our first six months of marriage, my husband and I had never discussed our feelings about beets. Then again, I had never made beets for him before. When I did, they were meant to bulk up a brimming vat of stew that would feed us every night for a week. In my husband’s version of the story, it lasted for three weeks. “I hope you like beets,” I announced that evening. “I may have added too many.”

Whether you love or hate beets, it is probably because they taste like dirt. Some people (my husband) can’t get over the flavor, and others can’t get enough of it. Some people experience beeturia, the appearance of bright red or hot pink urine after they eat red beets. Maybe this sight unsettles you. Or maybe you embrace the opportunity to track the transit of beet pigments through your body. You may admire their lovely rings and be inspired by the rich and brilliant colors that beets bring to salads. Or you might have picked up a lifelong aversion after too many canned pickled beets on a school lunch tray. Beets are a pretty polarizing vegetable. If you are among the haters, I’m going to do my best to turn the beet around for you.

Red and white beets

Why beets taste like dirt

Beets taste like dirt because they contain a compound called geosmin (meaning “dirt smell”). Geosmin is produced in abundance by several organisms that live in the soil, including fungi and some bacterial species in the genus Streptomyces. Humans are extremely sensitive to low concentrations of geosmin – so much so that we can smell it floating in the air after rain has stirred it up from the soil (Maher & Goldman, 2017). While people generally like that rain-fresh scent in the air, it’s less welcome elsewhere. For example, we perceive it as an off taste in water drawn from reservoirs with a lot of geosmin-producing cyanobacteria. In wines, geosmin contributes to cork taint. Continue reading

Kiwifruit 2: Why are they green?

Why are some kiwifruits green when they are ripe? Or avocados or honeydew melons? The answer involves genetic accidents, photosynthesis, hidden pigments, and the words “monkey peach.”

In our kiwifruit fuzziness essay we described how the type and density of trichomes—the hairlike projections from the fruit’s skin that create the fuzziness—in the Actinidia chinensis species complex is correlated with the habitat in China to which a particular population is adapted and the ploidy level of its genome. Only polyploid (having multiple genome copies) Actinidia chinensis occupy the harshest environments—the high, arid reaches of western China—and have the highest trichome density and the longest trichomes. And those fuzzy, resilient, polyploid kiwifruits are all green on the inside (1). They are the plant kingdom’s version of an unshaved vegan after backcountry skiing for a week. The hardy plant had no trouble growing outside its plateau of origin and became the most common commercial kiwifruit in the world (A. chinensis var. deliciosa), followed closely by yellow-fleshed (“golden”), less fuzzy variants of the same species (A. chinensis var. chinensis).

An expanded view of the dozens of Actinidia species reveals orange, red, and purplish pigments that color fruits in the genus. While beautiful, this warm palette strikes me as noteworthy only in contrast to the bright green displayed by the fuzzy A. chinensis var. deliciosa that initially grabbed my attention, and, later, in green kiwiberries (A. arguta). A non-green (for lack of better terminology, “colorful”) ripe fruit, after all, is a common end point for species with fleshy fruit.

Fig. 1 from Crowhurst et al. (2008) of some fruit diversity in the kiwifruit genus Actinidia. We describe the botany and anatomy of kiwifruits in our kiwifruit fuzziness essay.

It is not difficult, however, to bring to mind other examples of species with green-ripe fruit: avocado, green grapes, some citrus, honeydew melon (I’m specifically thinking here of the pericarp or mesocarp tissue under the skin and exclude from this discussion immature fruits that lose their greenness when fully ripe, like green beans and olives). Green ripe fruit, then, in Actinidia and other taxa, seems to me to be something to explain. What, if any, function might it serve, and what are the mechanisms responsible?

While the literature on the subject is far from exhaustive, there is a fairly pedestrian explanation at least for the mechanism, if not any adaptive function, of unusually green fruit flesh outside of Actinidia: fruits start green, and straightforward mutations in a few key genes cause them to remain so. Like that intrepid, hirsute montane vegan, though, Actinidia performs the task a little differently, and it is a bit of a mystery. To understand why that is, we need some backstory on pigments in fruit and how and why they change as fruit ripens, with a focus on Actinidia. Continue reading

Kiwifruit 1: Why are they so fuzzy?

Kiwifruit is not covered in hairs. It’s covered in trichomes. And only if you’re talking about green Actinidia chinensis var. deliciosa. But, why? One answer is: pretty much to keep it from drying out. Another is: because it’s a polyploid from western China and was kind of chosen at random to be the most commonly grown kiwifruit, and they’re not all fuzzy. Those aren’t mutually exclusive answers. Put on your ecophysiology hats and grab a paring knife.

Think of fruit growth as a balancing act between ingoing and outgoing fluxes. When the balance is positive, fruits grow. When it is negative, they shrink—or shrivel. The main fluxes in question are carbon and water, which enter the fruit from the xylem and phloem of the plant vascular system. Water is lost mainly to the atmosphere via transpiration (evaporative water lost through stomata and other pores and from the skin surface). Keeping the ledger positive isn’t an easy job for a fruit. Hot, dry, and windy weather encourages transpiration and thereby increases the odds that a fruit will experience water stress. Excessive sunlight may cause sunburn. Fruits also need to avoid attack from pathogens and herbivores before the seeds within mature. A fruit’s skin—its cuticle and epidermis—is its first line of defense against abiotic and biotic threats. Some fruits resort to creative coverings to get the job done.

Here I’ll take a close look at the skin of kiwifruits. Why, exactly, are they so fuzzy?

A heart-shaped green kiwifruit (Actinidia chinensis var. deliciosa), covered in fuzzy trichomes

Continue reading

Botany Lab of the Month: Jack-O-Lantern

Happy National Pumpkin Day! Turn carving your Halloween Jack-O-Lantern into a plant dissection exercise.


The first Jack-O-Lanterns were carved out of turnips in 17th-century Ireland. While the large, starchy hypocotyls (fused stem and taproot) of cruciferous vegetables are anatomically fascinating, this post will be about the stuff you are more likely cutting through to make a modern Jack-O-Lantern out of squash. Continue reading

Botany Lab of the Month, Presidential Inauguration Edition: Saffron

If you like your spices gold-colored and expensive, find some fresh Crocus sativus flowers and grab ‘em by the…disproportionately large female reproductive organ. Small hands might work best, though it might turn your skin orange. Saffron is probably from the Middle East. If that bothers you, you may want to ban it from your spice shelves, however ill that bodes for the quality of your cabinet. After all, there is a stigma against that sort of thing.

The most expensive oversized reproductive organ in the world


A pile of dried saffron stigmas (“threads”). Photo from Wikipedia

You may know that saffron is the most expensive spice in the world. A Spanish farmer sold his crop of high quality saffron this year for four euros per gram, which is a ninth of today’s price of gold (36 euros per gram). Saffron is expensive because its production requires a huge amount of labor and land. Saffron production is labor- and land-intensive because saffron is a botanically unique food item that defies mechanical harvest and accounts for a miniscule proportion of the plant that bears it. The saffron threads sold as spice are the dried stigmas of the flowers of the saffron crocus (Crocus sativus, family Iridaceae). Recall that the stigma is the part of the flower’s female reproductive organs that catches pollen. Pollen travels from the stigma through the style into the flower’s ovary (collectively, the stigma, style, and ovary comprise the pistil). Continue reading