Inside of a Seed: Two Monocots

“Seeds are travelers in space and time – small packages of DNA, protein, and starch that can move over long distances and remain viable for hundreds of years. These packages have everything they need not only to survive, but also to grow into a plant when they encounter the right conditions.”      The Book of Seeds by Paul Smith


As illustrated in last week’s post, the mature seeds of dicots – depending on the species – can be either with or without endosperm (a starchy food packet that feeds a growing seedling upon germination). Seeds without endosperm store these essential sugars in their cotyledons. Monocotyledons (or monocots, for short) are a group of flowering plants (i.e. angiosperms) whose seedlings are composed of a single cotyledon. With the exception of orchids, the seeds of monocots always contain endosperm.

The first of two examples of monocot seeds is the common onion (Allium cepa). The embryo in this seed sits curled up, surrounded by endosperm inside of a durable seed coat.

If you have ever sown onion seeds, you have watched as the single, grass-like cotyledon emerges from the soil. The seed coat often remains attached to the tip of the cotyledon like a little helmet as it stretches out towards the sky. Soon the first true leaf appears, pushing out from the base of the cotyledon. The source of this first leaf is the plumule hidden within the cotyledon.

The fruit of plants in the grass family – including cereal grains like wheat, oats, barley, rice, and corn – is called a caryopsis. In this type of fruit, the fruit wall (or pericarp) is fused to the seed coat, making the fruit indistinguishable from the seed. The embryos in these seeds are highly developed, with a few more discernible parts. A simplified diagram of a corn seed (Zea mays) is shown below. Each kernel of corn on a cob is a caryopsis. These relatively large seeds are great for demonstrating the anatomy of seeds in the grass family.

In these seeds there is an additional layer of endosperm called aleurone, which is rich in protein and composed of living cells. The cells of the adjacent endosperm are not alive and are composed of starch. The embryo consists of several parts, including the cotyledon (which, in the grass family, is also called a scuttelum), coleoptile, plumule, radicle, and coleorhiza. The coleoptile is a sheath that protects the emerging shoot as it pushes up through the soil. The plumule is the growing point for the first shoots and leaves, and the radicle is the beginning of the root system. The emerging root is protected by a root cap called a calyptra and a sheath called a coleorhiza.

Germination begins with the coleorhiza pushing through the pericarp. It is quickly followed by the radicle growing through the coleorhiza. As the embryo emerges, a signal is sent to the endosperm to start feeding the growing baby corn plant, giving it a head start until it can make its own food via photosynthesis.

corn seeds (Zea mays)

Up Next: We’ll take an inside look at the seeds of gymnosperms.


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What Is a Plant, and Why Should I Care? part four

What Is a Plant?

Part one and two of this series have hopefully answered that.

Why should you care?

Part three offered a pretty convincing answer: “if it wasn’t for [plants], there wouldn’t be much life on this planet to speak of.”

Plants are at the bottom of the food chain and are a principle component of most habitats. They play major roles in nutrient cycling, soil formation, the water cycle, air and water quality, and climate and weather patterns. The examples used in part three of this series to explain the diverse ways that plants provide habitat and food for other organisms apply to humans as well. However, humans have found numerous other uses for plants that are mostly unique to our species – some of which will be discussed here.

But first, some additional thoughts on photosynthesis. Plants photosynthesize thanks to the work accomplished by very early photoautotrophic bacteria that were confined to aquatic environments. These bacteria developed the metabolic processes and cellular components that were later co-opted (via symbiogensis) by early plants. Plants later colonized land, bringing with them the phenomena of photosynthesis and transforming life on earth as we know it. Single-celled organisms started this whole thing, and they continue to rule. That’s just something to keep in mind, since our focus tends to be on large, multi-cellular beings, overlooking all the tiny, less visible beings at work all around us making life possible.

Current representation of the tree of life. Microorganisms clearly dominate. (image credit: nature microbiology)

Current representation of the tree of life. Microorganisms clearly dominate. (image credit: nature microbiology)

Food is likely the first thing that comes to mind when considering what use plants are to humans. The domestication of plants and the development of agriculture are easily among the most important events in human history. Agricultural innovations continue today and are necessary in order to both feed a growing population and reduce our environmental impact. This is why efforts to discover and conserve crop wild relatives are so essential.

Plants don’t just feed us though. They house us, clothe us, medicate us, transport us, supply us, teach us, inspire us, and entertain us. Enumerating the untold ways that plants factor in to our daily lives is a monumental task. Rather than tackling that task here, I’ll suggest a few starting points: this Wikipedia page, this BGCI article, this Encylopedia of Life article, and this book by Anna Lewington. Learning about the countless uses humans have found for plants over millennia should inspire admiration for these green organisms. If that admiration leads to conservation, all the better. After all, if the plants go, so do we.

Humans have a long tradition of using plants as medicine. Despite all that we have discovered regarding the medicinal properties of plants, there remains much to be discovered. This one of the many reasons why plant conservation is so important. (photo credit: wikimedia commons)

Humans have a long tradition of using plants as medicine. Despite all that we have discovered regarding the medicinal properties of plants, there remains much to be discovered. This is one of the many reasons why plant conservation is imperative. (photo credit: wikimedia commons)

Gaining an appreciation for the things that plants do for us is increasingly important as our species becomes more urban. Our dense populations tend to push plants and other organisms out, yet we still rely on their “services” for survival. Many of the functions that plants serve out in the wild can be beneficial when incorporated into urban environments. Plants improve air quality, reduce noise pollution, mitigate urban heat islands, help manage storm water runoff, create habitat for urban wildlife, act as a windbreak, reduce soil erosion, and help save energy spent on cooling and heating. Taking advantage of these “ecosystem services” can help our cities become more liveable and sustainable. As the environmental, social, and economic benefits of “urban greening” are better understood, groups like San Francisco’s Friends of the Urban Forest are convening to help cities across the world go green.

The importance of plants as food, medicine, fuel, fiber, housing, habitat, and other resources is clear. Less obvious is the importance of plants in our psychological well being. Numerous studies have demonstrated that simply having plants nearby can offer benefits to one’s mental and physical health. Yet, urbanization and advancements in technology have resulted in humans spending more and more time indoors and living largely sedentary lives. Because of this shift, author Richard Louv and others warn about nature deficit disorder, a term not recognized as an actual condition by the medical community but meant to describe our disconnect with the natural world. A recent article in BBC News adds “nature knowledge deficit” to these warnings – collectively our knowledge about nature is slipping away because we don’t spend enough time in it.

The mounting evidence for the benefits of having nature nearby should be enough for us to want to protect it. However, recognizing that we are a part of that nature rather than apart from it should also be emphasized. The process that plants went through over hundreds of millions of years to move from water to land and then to become what they are today is parallel with the process that we went through. At no point in time did we become separate from this process. We are as natural as the plants. We may need them a bit more than they need us, but we are all part of a bigger picture. Perhaps coming to grips with this reality can help us develop greater compassion for ourselves as well as for the living world around us.

What Is a Plant, and Why Should I Care? part one

I want to tell the story of plants. In order to do that, I suppose I will need to research the 4 billion year history of life on earth. And so I am. Apart from satiating my own curiosity, studying and telling the story of plants advances me towards my goal of creating a series of botany lesson themed posts. Botany 101 and beyond, if you will. An ambitious project, perhaps, but what else am I going to do with my time?

So what is a plant anyway? We all know plants when we see them, but have you ever tried to define them? They are living beings, but they are not animals. They are stationary – rooted in the ground, usually. Most of them are green, but not all of them. They photosynthesize, which means they use water, carbon dioxide collected from the atmosphere, and energy harvested from the sun to make food for themselves. No animal can do that (okay…a few sort of can). They reproduce sexually, but many can also reproduce asexually. They are incredibly diverse. Some grow hundreds of feet into the air. Some barely reach more than a few centimeters off the ground at maturity. They have discernible parts and pieces, but they can also lose parts and pieces and then grow them back. There aren’t many animals that can do that. They have been on this planet for hundreds of millions of years, colonizing land millions of years before animals. Plants helped pave the way, and if it weren’t for plants, animals may not have stood a chance.

I don’t mean to pick on animals, it’s just that for a long time, humans grouped living things into just two kingdoms: Plantae and Animalia. Stationary things that appeared to be rooted to the ground or some other surface were classified as plants. Green things that lived in the water were also considered plants. Thus, lichens, fungi, algae, and everything we consider to be a plant today were placed in kingdom Plantae. Everything else was placed in kingdom Animalia. This, of course, was before much was known about microorganisms.

Dichotomous classification was reconsidered as we learned more about the diversity of organisms in each kingdom, particularly as the theory of evolution came into play and microscopes allowed us to observe single celled organisms and chromosomes. Eventually, fungi was awarded its own kingdom, which includes lichens – organisms composed of both fungi and photosynthetic species but classified according to their fungal components. Most of the algae was placed in a kingdom called Protista, a hodgepodge group of unicellular and unicellular-colonial organisms, some of which are animal-like and some of which are plant-like. Two kingdoms were also formed for prokaryotic organisms (organisms with cells that lack membrane bound organelles): Bacteria and Archaea.

Illustration of one current itteration of kingdom classification system (illustration credit: wikimedia commons)

Taxonomic kingdoms as we currently consider them (illustration credit: wikimedia commons)

In short, the answer to what is a plant seems to be whatever organisms humans decide to put in kingdom Plantae. One problem with this answer is that some chose to include certain species of algae and others don’t. But why is that? It has to do with how plants evolved and became photosynthetic in the first place.

Microorganisms developed the ability to photosynthesize around 3.5 billion years ago; however, the photosynthetic process that plants use today appeared much later – around 2.7 billion years ago. It evolved in an organism called cyanobacteria – a prokaryote. Eukaryotic organisms were formed when one single cell organism was taken inside another single cell organism, a process known as symbiogenesis. In this case, cyanobacteria was taken up and the eukaryotic organisms known today as algae were formed. The incorporated cyanobacteria became known as chloroplasts.

Not all algae species went on to evolve into plants. A group known as green algae appears to be the most closely related to plants, and a certain subset of green algae colonized the land and evolved into modern day plants (also known as land plants). That is why some taxonomists choose to include green algae in the plant kingdom, excluding all other types of algae.

Common stonewort (Chara vulgaris, a species of green algae (photo credit:

Common stonewort, Chara vulgaris, a species of green algae (photo credit:

The term land plants refers to liverworts, hornworts, mosses, ferns, fern allies, gymnosperms, and flowering plants – or in other words, all vascular and non-vascular plants. Another all encompassing term for this large group of organisms is embryophytes (embryo-producing plants).

Still confused about what a plant is? Three main features can be attributed to all plants: 1. They are multicellular organisms. 2. Their cell structure includes a cell wall composed of cellulose 3. They are capable of photosynthesis. Many species of green algae are unicellular, which is an argument for leaving them out of kingdom Plantae. Certain parasitic plants like toothwort, dodder, and beech drops have lost all or most of their chlorophyll and no longer photosynthesize, but they are still plants.

Deciding what is and isn’t a plant ultimately comes down to evolutionary history and common ancestry. As Joseph Armstrong writes in his book, How the Earth Turned Green, “Our classifications of human artifacts are totally arbitrary, but to be useful scientifically our classification of life must accurately reflect groupings that resulted from real historical events, common ancestries.”

Obviously this is going to be a multi-part series, so I will have much more to tell you about plants in part two, etc. For now, this You Tube video offers a decent summary.

Artificial Photosynthesis – A Case of Biomimicry

Humans have long sought solutions to their problems by observing nature and trying to mimic it. These endeavors have lead to improvements in the designs and production processes of countless things. In recent decades there has been a growing movement composed of scientists, engineers, and innovators of all types to expressly seek for answers to today’s most pressing problems by deeply observing and analyzing the natural world. These efforts are coupled with a desire to learn how to work with nature rather than against it in an attempt to secure a more sustainable future for life on Earth. This is the essence of biomimicry.

To this end, plants have much to teach us. Everything from their basic forms and functions to the way they fight off pests and diseases to the way they communicate with each other is worth exploring for biomimicry purposes. A plant-based phenomenon that has probably received the most attention – and for good reason – is photosynthesis, the process that enables plants to use the sun to make food.

Put another way, photosynthesis is the process of converting light energy into chemical energy. Specialized proteins in plant cells absorb particles of light which initiates the passing of electrons across a series of molecules. Subsequently, water is split by a protein complex into oxygen and hydrogen protons. The oxygen is released from the plant, while the electrons and hydrogen protons go on to help generate two compounds – NADPH and ATP – which are later used to power the reaction that transforms atmospheric carbon dioxide into sugars. The concept of photosynthesis, while fairly simple to grasp from a high level (i.e. light + water + carbon dioxide = sugars + oxygen), is actually quite complex, and there is still much too discover concerning it.

photo credit: wikimedia commons

photo credit: wikimedia commons

One thing is certain, photosynthesis is ubiquitous. As long as the sun is overhead, most plants, algae, and cyanobacteria are photosynthesizing at a steady clip and are thereby helping to power just about every other living organism on the planet. Without plants, most of the rest of us could not survive. Janine M. Benyus offers this human-centric view in her book Biomimicry:

Consider that everything we consume, from a carrot stick to a peppercorn filet, is the product of plants turning sunlight into chemical energy. Our cars, our computers, our Christmas tree lights all feed on photosynthesis as well, because the fossil fuels they use are merely the compressed remains of 600 million years worth of plants and animals that grew their bodies with sunlight. All of our petroleum-born plastics, pharmaceuticals and chemicals also spring from the loins of ancient photosynthesis. … Plants gather our solar energy for us and store it as fuel. To release that energy, we burn the plants or plant products, either internally, inside our cells, or externally, with fire.

Since plants are so well-versed in using sunlight to create food and energy, it only makes sense that we would look to them to learn how we might improve and expand upon our quest for renewable energy production. We already use the sun to produce electricity by way of photovoltaic systems; however, these systems are limited in that they can only produce electricity when the sun is shining, and electricity is difficult to store. Artificial photosynthesis involves using that electricity to power catalysts that can split water into hydrogen and oxygen. The hydrogen can be used as a fuel or can be fed into reactions involving carbon dioxide, ultimately resulting in a carbon-based fuel source. Fuels produced this way – referred to as solar fuels – could be stored and used regardless of whether or not the sun is out.

Artificial photosynthesis has largely moved beyond the theoretical stage. Multiple efforts have demonstrated ways in which water can be split using the light of the sun and solar fuels can thereby be produced. Mass production is the next step, and that is where the real limitations lie. The production of solar fuels has to be done cheaply enough to compete with other available fuels, and the infrastructure to use such fuels has to be available. These hurdles may very well be overcome, but it will take time. Meanwhile, research continues, adding to the mountains of studies already published.

photo credit: wikimedia commons

photo credit: wikimedia commons

On such study published in 2011 describes an “artificial leaf” that was developed at the Massachusetts Institute of Technology by Daniel Nocera and a team of researchers. Listen to an interview with Nocera on Science Friday and watch this BBC Worldwide video to learn more about this discovery. This Nature article explains why the artificial leaf is not yet commercially available, and why we are not likely to see it any time soon.

Another development in artificial photosynthesis was published earlier this year in Nano Letters. It is the product of Peidong Yang and the Kavli Energy NanoSciences Institute. While Nocera and his team stopped at the production of hydrogen gas, Yang’s lab added bacteria to the mix and were able to use the sun’s energy to transform carbon dioxide into acetate. If passed along to another species of bacteria, the acetate could be used to produce various synthetic fuels. Learn more about this by reading this livescience article and watching this FW: Thinking video. As with other artificial photosynthesis developments, limitations abound, but the research is promising.

Artificial photosynthesis is a compelling subject and one worth keeping an eye on. Follow the links below to learn more:

Biomimicry is an equally compelling subject and one I hope to explore further in future Awkward Botany posts. Meanwhile, check out these links:

Autumn Leaves

It’s October, so fall is in full force in the northern hemisphere. Days are shorter and temperatures are cooler, but one sure sign that fall is here is that the leaves on deciduous trees are changing colors. Every autumn, leaves that were once a familiar green turn brilliantly red, fiery orange, or vibrantly yellow. And then they fall to the ground leaving trees exposed – just trunks and branches  – skeletons of what they once were during warmer and brighter days.

But why?

Surprisingly enough, the colors seen in autumn are largely present in the leaves throughout their lives, but we don’t see them. We only see green. This is because chloroplasts (cell organelles responsible for carrying out photosynthesis) contain chlorophyll, one of three main pigments found in the cells of leaves throughout the growing season. Chlorophyll absorbs red and blue light and reflects green light. Because chloroplasts are so abundant in the cells of leaves, leaves look green.

But carotenoids are hanging around, too. The second of the three main pigments, carotenoids protect chlorophyll from oxidation and aid in photosynthesis. They reflect blue-green and blue light and appear yellow, however their population is considerably smaller compared to chlorophyll, so their yellow color is masked.

When day length decreases, the level of chlorophyll in plant cells diminishes. As a result, the yellow color of the carotenoids begins to show. Also, a layer of cells called the abscission layer forms between branches and petioles (i.e. leaf stems). This abscission layer is what eventually causes branches to drop their leaves. As the chlorophyll begins to die off and the abscission layer forms, anthocyanins (the third of the three main pigments found in plant cells) are synthesized. Anthocyanins absorb blue, blue-green, and green light and appear red.

With chlorophyll virtually absent (and photosynthesis brought to a halt) carotenoids and anthocyanins become the major pigments found in leaves, giving them the autumn colors we are accustomed to seeing. But here is where it gets tricky…

Fall leaf color is largely dependent on various environmental conditions, including temperature, amount of sunlight, and soil moisture. If autumn is warm and wet, chlorophyll may be slow to die, and anthocyanins may be slow to form. Chlorophyll drops off more readily when it is cool and dry, and anthocyanins synthesize more readily when days are sunny. Dry, sunny days followed by cool, dry nights are said to offer the most vibrant fall colors. Additionally, global climate change is now playing a role, so fall colors may start to appear earlier or later or last longer or shorter depending on the region.

Do you have a favorite place to view fall foliage? Add your comments below.


Cornus sericia – red-osier dogwood


Ribes aureum – golden current


Quercus palustris – pin oak


Fraxinus sp. – ash


Rhus sp. – sumac