272-Plant Science for Gardeners, Part II, with Robert Pavlis

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There is so much that we can learn about plant science to improve our understanding of how plants work, so gardener, writer and biochemist Robert Pavlis is back on the podcast this week for part two of our conversation on plant science for gardeners.

Robert is a plant collector with more than 3,000 species of plants, trees and shrubs at his private 6-acre botanical garden in southern Ontario, Canada. But he wasn’t always a plantsman. Robert is a chemist and biochemist by training who became a maker of laboratory software. He applies his science background to his gardening, and he uses his analytical experience to debunk the most persistent gardening myths. He is the publisher of and, and has authored several books, including Soil Science for Gardeners,“ “Building Natural Ponds,” “Best Garden Plants for Connoisseurs,” and his latest,  “Plant Science for Gardeners: Essentials for Growing Better Plants,” a great resource that presents scientific information in a way that’s easy for anyone to understand.


Robert Pavlis

Robert Pavlis has experience as a chemist and biochemist and he applies that background to gardening. He busts some of the most persistent garden myths and raises awareness of plant science among gardeners. (Courtesy of Robert Pavlis)


If you didn’t catch Part 1 of my conversation with Robert on plant science, you can listen to that episode now before diving into Part II. Robert’s also been a guest of “The joe gardener Show” in the past to discuss houseplant myths and garden products you don’t need

Before going any further, let me take a moment to remind you that I have a book of my own coming out in September. The title is “The Vegetable Gardening Book: Your complete guide to growing an edible organic garden from seed to harvest,” and it’s available for pre-order now. It’s chock full of insider tips and new-to-you information that will help you step up your gardening game and tackle challenges. 

And on tap for 2023 is my new Online Gardening Academy™ premium course, Organic Vegetable Gardening. Sign up for the waitlist here.

The Architecture of a Leaf: Stomata & Leaf Margins

In a diagram of a leaf, there’s a lot there, and it can make your eyes glaze over. There are vertical, horizontal and circular lines, and layers and layers, and they all have a role to play. Fortunately, Robert breaks it down.

The most important layer is the surface layer, Robert says. It’s quite like the upper layer of human skin in that it looks fairly solid but actually has pores. The largest openings in a leaf are called stomata, and for the most part they are too small to see without a magnifying glass or microscope. They are mostly found on the underside of leaves, though there are a few up stoma on top. 

“They’re really important for the way the whole leaf works,” Robert says. “We can think of a stomata as kind of like our mouth in some ways because plants photosynthesize, and for that to work, they need CO2  from the air. And that CO2 comes in through the stomata, and the leaf can open and close these things depending on different conditions.”

At night, when a plant’s not photosynthesizing, the stomata tend to close up. When a plant is photosynthesizing and needs more carbon dioxide, the stomata open up.

Stomata are also one of the places where plants expel excess water. Robert says plants need water for the chemical reaction that takes place through photosynthesis, but when a plant has taken up more water than it can use, that water needs to go somewhere.

“We can think of the whole plant as kind of being a giant straw,” Robert says. At the bottom end are roots sucking in water, and at the upper end are stomata in the leaves letting the water out. There is a constant flow of water going up the plant. 

The roots act independently of the stomata, continually sucking up water, which is then drawn up the xylem. That upward pressure helps a plant keep its turgor — a botanical term for rigidity of cells and tissue. When a plant can’t take up water as fast as it expels water, it loses its turgor and droops.

You may be wondering why the stomata wouldn’t close up to keep water in, but there’s a good reason why water gets released. Stomata need to breathe carbon dioxide and exchange oxygen — to transpire. If the stomata keep closed in high heat to retain water, they can’t transpire.

At night, after the stomata stop photosynthesizing for the day and close up, water does have another way out if the pressure gets to be too much. Water can exit through the leaf margins. 

In one of the talks that Robert gives, he has a section called “The Crying Plants” in which he shows pictures of water as well as sugars oozing out of leaves. 

“Those are there so that the leaf doesn’t explode,” Robert says of the openings. “Basically, the leaf’s closed and it’s saying, ‘I don’t want any more water.’ And the root keeps saying, ‘Well, I’m gonna give you some water anyways.’ And then we have this safety valve that opens up and lets this stuff ooze out.”

In orchids, the moisture comes out of the center of leaves rather than the margins, and a sugary deposit is left on the underside. 



Orchids expel water and sugar from the center of the leaf rather than the leaf margins, and a sugary residue accumulates on the underside of the leaf. (photo: Courtesy Robert Pavlis)


The Architecture of a Leaf: The Outer Layers

The outer layers of a leaf, the epidermis, are quite tough and made from a different type of tissue than what’s found in the inner layers, Robert says. The tougher the outer layers are, the greater protection they offer from pests.

For example, blue hosta leaves have tougher outer layers than a typical hosta, so they don’t suffer from slug damage like many hostas do. Another type of pest known as leaf miners gets inside leaves of various plants and burrows through the inner tissue without really damaging the top and bottom of a leaf.

When pesticides or foliar fertilizers are sprayed on leaves, the tough outer layers keep them from getting inside the leaves, for the most part. That’s why Robert says foliar feeding isn’t an effective way to fertilize plants, and he notes that pesticide sprays really won’t affect leaf miners for the same reason. 

The epidermis’ protective qualities also include protecting the leaves from too much UV light causing damage. 

“We can think of this layer as kind of like our windows,” Robert says. “We have to let a certain amount of light in, or the plant can’t photosynthesize. But UV rays can be harmful to the plant so it tends to exclude those. And it also filters out to some extent the wavelengths that actually get in.”

Most leaves are green because they are reflecting green wavelengths back to our eyes, he points out. The blue and red wavelengths get into the leaves and photosynthesize. It was once thought that plants don’t absorb green light because they reflect so much of it, but we now know that some green light is important for plants, Robert says. 

“They really want a combination of different wavelengths, but it’s the blue and red light that they use the most to photosynthesize and make their food,” he explains. “But these other colors also are used in other ways.”

Wavelengths such as green and infrared trigger certain things in the plant, so plants really do want the whole spectrum of light. 


green leaves

Green leaves reflect green wavelengths while blue and red wavelights enter leaves and help plants perform photosynthesis. It was once thought that plants don’t absorb green light because they reflect so much of it, but we now know that some green light is important for plants for function, Robert says.  (Courtesy of Robert Pavlis)


Why Plants Need to Be Hardened Off

When plants that were started indoors are being readied for a move outdoors, they need to be hardened off to condition them to the intensity of direct sunlight. Under indoor grow lights, they are getting a lot of blue and red light, but the sun is more intense than grow lights by a factor of 10. 

Robert says that plants in low light tend to make their protective membrane thinner so more light can get through. This is why moving an indoor plant outside into the sun can cause great damage within just a few hours. The plant doesn’t have time to develop an adequate protective membrane, and in effect, the plant becomes sunburned by the intensity of blue and red light from the sun as well as the UV sunlight that it never received while indoors. 

To properly harden off a plant, put it out for just a half hour on its first day outdoors, then an hour the next day, and gradually increase the time spent in full sun by an hour a day until the plant can withstand a full day’s worth of sunlight. 

The existing leaves change somewhat in the sun but not completely. Robert says it’s the next set of leaves that grow that will have a thicker cuticle and will have a different texture and color. The new leaves may also be smaller or larger.

“The plant’s always trying to get as much light as it can without damaging itself,” Robert says.


Shade cloth over seedling trays

One way to effectively harden off seedlings is to cover them with row cover to add extra protection from the harsh sun.


The Architecture of a Leaf: Trichomes

Trichomes are extensions of leaves, like leaf hairs. “Trichomes are different depending on the type of plant we’re looking at,” Robert says.

For plants like cacti that live in high light, high UV environments, trichomes protect the plant, keeping the temperature a little lower and the UV exposure down — basically shading the plant.

Some trichomes act as defense mechanisms. For example, trichomes can make leaves fuzzy, and deer tend to leave fuzzy leaves alone because they don’t taste good.

A new discovery about trichomes is that they may be a center of fixing nitrogen.

“Some of the latest research shows that trichomes have nitrogen-fixing bacteria inside of them, and the plant may be making the trichomes a lot of times just to get nitrogen,” Robert says. “So these nitrogen-fixing bacteria are living inside the trichomes, inside these hairs, and they’re actually moving around.  And then periodically the plant ejects them because this environment’s not really good for bacteria. They’re slowly dying. So the plant then ejects them, lets them recuperate, and then it sucks them back in again and uses them to make nitrogen.”

A hair on a leaf is huge compared to a bacterium, Robert notes. When the bacteria is ejected, it sits on the outside of the hair, where it can get oxygen and recuperate. The plant then takes the bacteria back in, uses it for nitrogen for a few days, and when the bacteria start to die again, it lets the bacteria back out to recuperate. The leaf is basically managing a herd of microbes.

“We look at those leaves, and they look so shiny and clean, and they’re just covered with all kinds of microbes on the outside, you know, fungal spores and thick, thick layers of bacteria and all these organisms living on there,” Robert says. 

The leaf surface also affects what pests browse on plants, from pests as big as deer down to mites. Aphids might be found on some plants and not others because of what’s on the leaves’ surface — and taste is another factor.  “Leaves are constantly making thousands of different chemicals so they all have different flavors and they have different tastes” that attract or dissuade predators, Robert says. 

What we as humans can smell and what we think of as fragrant is only part of what’s out there. Animals, particularly insects, smell and sense in ways that we can’t. They detect smells in leaves that we’d never know are there.

Issues with Insecticidal Soap

Robert has been telling gardeners for years not to use soaps from their house while making insecticidal soap. Household soaps are sodium based, and sodium is quite toxic for plants. 

The outside layer of leaves, known as the cuticle layer, has a waxy or oily coating that provides protection. Dish soap dissolves those waxy or oily cuticles and washes off that protective layer. Now all sorts of pathogens have an easier time getting into the leaves.

“Most of the things we have in the house that we call soaps are really not soaps. They are detergents, which are even worse,” Robert says. “I don’t know where Dawn got its reputation for being safe for plants, but it really isn’t.” 

How Leaves Adjust to Get the Light They Need

A plant needs a certain amount of light to make the food it needs to grow, and it makes adjustments to increase the amount of light — up to a certain level, Robert says.

Think of a small leaf and a large leaf that are otherwise identical. The large leaf, with its additional surface area, will collect more light. So if a plant wants more light, it will produce larger leaves.

Another thing a plant can do is change how it orients its leaves. It can use its petioles — the stalk that joins a leaf to a stem — to flip the leaves during the day to face the sun. Plus, as a plant gets larger, it concentrates its leaf growth on the top of the plant, closest to the sun. Many plants drop their lower leaves that are now shaded.

“Leaves have a lifespan,” Robert says. “And it’s not the lifespan of the plant. So a plant makes these leaves and this leaf might live for a week or a month or six months, depending on the plant. But at some point it’s old and it doesn’t work anymore. So the plant gets rid of it.”

New leaf growth may also be patterned to allow more light to reach the lower leaves.  “They usually don’t grow the next set of leaves above the previous set,” Robert says. Instead, they grow in between the previous sets. One layer of leaves may face north-south, while the next is east-west, and growth continues to alternate. 



Plants pattern their growth so new leaves won’t block light to the leaves immediately below them. It’s one way plants ensure they get the light they need to perform photosynthesis. (Courtesy of Robert Pavlis)



For a plant to maintain turgor, it needs to move an adequate amount of water up its stem to the leaves. When a plant doesn’t have enough water in its stem, that doesn’t always mean that there is not enough water in the soil. The problem could be that the leaves are losing water faster than the roots can supply.

“So the physical view of the plant looks the same in both cases,” Robert says. “One case, the soil is dry, and in the other case, the soil is wet. The problem is most gardeners think they have to water.”

In one case, watering can help, in another, too much water can drown the roots. 

The issue could be that something has happened to the roots. If the root system is half the size it should be — this could be due to disease, transplanting, or digging — there is no way that the plant can pump enough water. It doesn’t have enough root tips to move the water that’s needed.

Robert’s rule is to water because the soil is dry, not because the leaves are droopy. Droopy plants will usually recover overnight, when it’s cooler, the leaves need less water, and the roots can catch up. 


turgor example

Plants stand tall and resist drooping due to turgor pressure, caused by the upward movement on water from the roots to the stems and leaves.(Courtesy of Robert Pavlis)

How Plants Communicate

Robert does not like anthropomorphizing plants. Plants don’t think and don’t have intelligence, he says. That’s why he doesn’t like reading articles that say plants “talk” to each other. He prefers more accurate terminology: Plants use chemical signaling. 

For example, a bug comes along and sits on a plant’s leaf and chews it. The plant can sense that chewing damage due to chemical reactions that the chewing triggers. The other leaves sense that chemical as it floats out in the air.

“Other leaves on this plant sense that chemical,” Robert says. “They in effect smell it, and they start producing a natural pesticide.”

As more leaves produce the pesticide, other leaves sense it and do the same, and the chemical signal eventually reaches the plant next to it, which, if it’s the same kind of plant, also produces the natural pesticide.  

“So now this bug leaves this leaf and goes over to another one that looks juicier, and suddenly it doesn’t taste so good because there’s a pesticide in now,” he says. “It could be a harmful pesticide. It could be a chemical that just makes the plant taste bad. It could be a chemical that hides the fragrance of the leaf and so on. There’s a variety of combinations.”

The same idea works to protect plants from diseases. Roberts notes that most study in that realm has focused on insect predators rather than pathogens because it can take weeks for a fungal infection to show. But he does know that studies show that when a fungus attacks a plant’s roots, the roots put out signaling chemicals that can reach other plants in the areas and associated fungi. 

Monarchs and Plant Chemicals

Monarch butterflies, which were recently declared endangered, are a classic example of the relationship between plant chemicals and insects.

Plants in the Asclepias genus are monarch larvae host plants. They are known as milkweed because of a latex substance they produce that makes them unappealing to most insects. The substance not only tastes bad — it’s toxic. But monarchs have evolved to be able to stomach the substance.

“It’s actually not good for the monarch either, but it doesn’t harm the monarch enough to keep it from eating it,” Robert says.

By author Dr. Anurag Agrawal, the book “Monarchs and Milkweed” explains in depth this fascinating evolutionary relationship. 


Monarch caterpillar eating milkweed

Monarch butterfly larvae exclusively feed on plants in the Asclepias genus. These plants, known as milkweeds, produce a substance that repels most insects, but Monarch caterpillars can stomach it. (photo: Amy Prentice


Abiotic Stress

Pests and pathogens are living things that can cause plants stress. The nonliving factors that can cause plants stress, such as drought, nutrient deficiency, extreme temperatures and salinity, are called abiotic stress. 

If you grow tomatoes, you may have come across reddish or purplish leaves at some point. This is due to abiotic stress that causes the plants to produce a red pigment.  Nailing down the triggering stress can be difficult. Robert suspects the red is there to reduce how much red light a plant receives, like sunscreen to cut down how much light a stressed plant takes in. 

When the stress is gone, a plant should revert to its normal growth habits.


Plant Science for Gardeners Book

Robert’s new book, “Plant Science for Gardeners,” is a great resource and easy for the lay person to understand. (Courtesy of Robert Pavlis)


I hope you enjoyed part two of my conversation with Robert Pavlis. If you haven’t listened yet, you can hear this episode now by scrolling to the top of the page and clicking the Play icon in the green bar under the page title. 

How has understanding plant science helped you become a better gardener?  Let us know in the comments below.

Links & Resources

Some product links in this guide are affiliate links. See full disclosure below.

Episode 048: The Simple Science Behind Great Gardening, with Lee Reich

Episode 083: Gardening Indoors: The Science of Light, with Leslie Halleck

Episode 116: Understanding the Soil Food Web, with Dr. Elaine Ingham

Episode 139: Houseplant Myths: The Facts Behind Caring for Indoor Plants

Episode 143: Gardening Products You Don’t Need, and Why

Episode 147: Monarchs and Milkweed: A Precarious Struggle Between Life and Death

Episode 153: The Science Behind Great Soil

Episode 179: Plant Partners: The Science-based Benefits of Companion Planting, with Jessica Walliser

Episode 223: How Soil Microbes Make Good Soil Great

Episode 270: Plant Science for Gardeners, with Robert Pavlis, Part I

joegardenerTV YouTube: How to Get the Best Drainage for Your Container – Why What You’ve Been Taught Is All Wrong

joegardener Online Gardening Academy™: Popular courses on gardening fundamentals; managing pests, diseases & weeds; seed starting and more.

joegardener Online Gardening Academy Organic Vegetable Gardening: My new premium online course membership opens in 2023. Sign up for the waitlist here.

joegardener Online Gardening Academy Beginning Gardener Fundamentals: Essential principles to know to create a thriving garden.

joegardener Online Gardening Academy Master Seed Starting: Everything you need to know to start your own plants from seed — indoors and out. 

joegardener Online Gardening Academy Growing Epic Tomatoes: Learn how to grow epic tomatoes with Joe Lamp’l and Craig LeHoullier. 

joegardener Online Gardening Academy Master Pests, Diseases & Weeds: Learn the proactive steps to take to manage pests, diseases and weeds for a more successful garden with a lot less frustration. Just $47 for lifetime access!

joegardener Online Gardening Academy Perfect Soil Recipe Master Class: Learn how to create the perfect soil environment for thriving plants.

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Growing a Greener World®     


Garden Fundamentals on YouTube

Garden Fundamentals Facebook group

Building Natural Ponds Facebook group

Plant Science for Gardeners: Essentials for Growing Better Plants” by Robert Pavlis

Soil Science for Gardeners: Working with Nature to Build Soil Health” by Robert Pavlis

Building Natural Ponds: Create a Clean, Algae-free Pond without Pumps, Filters, or Chemicals”  by Robert Pavlis

Best Garden Plants for Connoisseurs: The best plants from my collection of over 3,000 garden gems” by Robert Pavlis

Garden Myths: Book 1” by Robert Pavlis

Garden Myths: Book 2” by Robert Pavlis

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Disclosure: Some product links in this guide are affiliate links, which means we get a commission if you purchase. However, none of the prices of these resources have been increased to compensate us, and compensation is not an influencing factor on their inclusion here. The selection of all items featured in this post and podcast were based solely on merit and in no way influenced by any affiliate or financial incentive, or contractual relationship. At the time of this writing, Joe Lamp’l has professional relationships with the following companies who may have products included in this post and podcast: Rain Bird, Corona Tools, Milorganite, Soil3, Greenhouse Megastore, PittMoss, Territorial Seed Company, Earth’s Ally and TerraThrive. These companies are either Brand Partners of and/or advertise on our website. However, we receive no additional compensation from the sales or promotion of their product through this guide. The inclusion of any products mentioned within this post is entirely independent and exclusive of any relationship.

About Joe Lamp'l

Joe Lamp’l is the creator and “joe” behind joe gardener®. His lifetime passion and devotion to all things horticulture has led him to a long-time career as one of the country’s most recognized and trusted personalities in organic gardening and sustainability. That is most evident in his role as host and creator of Emmy Award-winning Growing a Greener World®, a national green-living lifestyle series on PBS currently broadcasting in its tenth season. When he’s not working in his large, raised bed vegetable garden, he’s likely planting or digging something up, or spending time with his family on their organic farm just north of Atlanta, GA.

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