Nature: The Original Chemist

We frequently see a contrast drawn between what is “natural” and what is “chemical.” Sometimes products are described as “chemical-free” even though every physical object is made of chemicals. As much as this suggests a problem with our science education, it speaks to a missed opportunity for wonder. Nature is not some sort of cosmic mother figure; on the contrary, nature is composed of diverse biological and physical processes, including some pretty amazing examples of chemistry continually taking place. If we indulge the human personification of nature and it’s “children” a bit, we could say the following about these “chemists:”

  • They are extremely creative.
  • They can make really complex molecules.
  • Some of their chemicals last a really long time – which is sometimes good and sometimes bad.
  • They are really good at making polymers.
  • They make some extremely toxic things.


I’ll give a few examples below.


Creative Natural Chemistry


The diversity of naturally occurring chemicals is staggering. Humans regularly take advantage of this, particularly when we need ideas for things like pharmaceuticals or crop protection products. Sometimes we extract the chemicals from a plant or other living thing. Often we grow tanks of microbes to harness their ability to make a chemical we find useful. In cases where the amounts of the chemical are too small to be practical from the natural source, human chemists can synthesize the same compound to fulfill the quantity needed. An example of this is a new potato sprout inhibitor. In many other instances, a natural chemical serves as the inspiration for human chemists to experiment with similar structures leading to the discovery of particularly useful drugs, fungicides, etc.


Taxol structure image by Calvero. Pacific Yew tree image by Jason Hollinger via creative commons. Azoxystrobin fungicide structure by Yikrazuul.   Strobilurus tenacellus mushroom picture by Tatiana Bulyonkova at Mushroom Observer.



Complex Natural Chemistry


Some of the most abundant chemicals in nature are simple. Nearly 80% of the air we breathe is nitrogen in the form, N2 – just two nitrogen atoms bonded together. Nitrogen goes through natural cycles that are important to all living things but often stays in relatively uncomplicated forms like ammonia (NH3) or nitrate (NO3). On the other hand, natural chemicals can be complex, so much so that it would be challenging for even a skilled human chemist to make them.


One of these complex examples is called spinosad and it is produced by a microbe called an actinomycete. We have found this to be a particularly effective insecticide for use on crops yet quite benign for the environment and not toxic to people. The chemical company that produces this for farmers relies on the natural microbe to produce this complicated bit of chemistry.


Structure of Spinosyn image by Capaccio via creative commons.


Long-Lived Natural Chemicals


Most naturally occurring chemicals are part of a cycle in which chemicals combine, making a material, but then eventually break back down into basic constituents to begin the cycle again. Some naturally produced chemicals are relatively long-lived. This can be a good thing in the case of the chemicals that are found in the organic matter of a healthy, undisturbed soil. These are not just any plant or microbial product; they are specific compounds that slowly cascade through a series of breakdown products.


For instance, plants make a group of complex, phenolic chemicals, called lignin, which are important for strengthening their cell walls. Lignin is quite resistant to microbial breakdown, although some fungi can and do destroy it, even as they decompose wood. Lignin is a major component of what is termed humus – the component of soil that helps to buffer nutrients and retain moisture. When soils are converted from wild land to cultivation, there is a dramatic increase in the rate of breakdown of these chemicals and thus the release of the carbon dioxide.


Some long-lived, natural chemicals, however, are less desirable. Under low oxygen conditions, soil-dwelling microbes can interconvert forms of nitrogen (e.g. ammonia to nitrate or nitrate to nitrogen gas). In that process, they “accidentally” make some nitrous oxide (N2O). Nitrous oxide is around 300 times more potent than carbon dioxide as a greenhouse gas because it lasts longer in the atmosphere. Unfortunately, human activity can exacerbate the production of this naturally generated chemical from farmed soils. Adjustments in farming practices can lead to a better balance of the production of natural chemicals that help or hurt greenhouse gas levels.



Fancy Polymeric Natural Chemicals


In the 1967 movie The Graduate, the character played by Dustin Hoffman is lectured about how the future is going to be all about plastics. Indeed, many people were excited in that era about polymers that chemists were developing, like nylon and polyester. These are based on long chains of monomers attached end to end.


Many of the most abundant natural chemicals on earth are also polymers, which are long chains made of simple sugar molecules. Depending on which sugar and how the sugars are linked together, the polymers result in anything from the cellulose that makes cotton fiber to wood or even the alginate from seaweed we use for thickening foods or the starch that is the primary energy source in foods like pasta, bread, rice or potatoes. Increasingly, we are tapping in to the enzymatic tools found in microbes in order to make polymers from renewable resources.


Variously Toxic Chemistries


Most people associate the term natural with the terms safe and wholesome. This impression has been created by decades of marketing, not by any understanding of the chemicals in nature. Many natural chemicals are perfectly benign; however, nature’s assortment of chemicals also includes many that are toxic by various mechanisms.  Lots of plants make chemicals to protect themselves from being eaten or otherwise bothered. We have all heard about nasty plants like poison ivy or even lovely plants like the Colorado Columbine which are dangerous to eat.


Cut Granny Smith apple image from Wikimedia. Cauliflower image from Calliope via creative commons. Hot pepper image by Andre Karwath via creative commons. Capsaicin structure by Jurgen Martens. Nicotine structure by NEUROtiker. Cyanide structure via Wikimedia.

Food plants also make some fairly toxic chemicals. The seeds of many familiar crops, including apples, cherries and peaches to name a few, contain a chemical storage component called a cyanogenic glycoside. When the seed is damaged, enzymes release hydrogen cyanide from the glycoside. Hydrogen cyanide is very toxic! It is a good reason not to eat those seeds, although it would take a lot of such seeds to hurt a person. The capsaicin that we enjoy in hot sauce is an insect protection chemical made by the pepper plant to defend itself. It is moderately toxic to us but not at the doses we normally consume. Quite a few plants make nicotine to ward off insects including tomatoes, cauliflower and eggplant. Nicotine is very toxic but not at the doses these crops produce. As with any toxic chemical, natural toxins are only an issue to humans at a certain dose.


Some natural chemicals, however, are extremely dangerous and we don’t want those in our food. Mycotoxins are a particularly nasty category of natural chemicals produced by certain fungi. One such chemical, called aflatoxin, is among the more toxic chemicals in existence and is also a potent carcinogen. Unfortunately, under certain circumstances, fungi can produce aflatoxin in food crops. In the developed world, a system of controls and testing keeps us well protected from this; in the developing world, though, aflatoxin is a major cause of death both through acute and chronic effects because it contaminates staple foods like corn or groundnuts.


Aspergillus infected groundnut image from International Institute of Tropical Agriculture. Aflatoxin structure by Ju


Some natural chemicals are elegantly selective in their toxicity. A soil bacterium, called Bacillus thuringiensis (usually called “Bt”), makes proteins that are specific in their toxicity to only certain categories of insects. One strain of Bt makes proteins that only effect beetles while another’s toxin only affects caterpillars. None of these Bt proteins are toxic to humans or almost anything else. We have made excellent use of these natural chemical toxins as sprayable insect controls and by genetically engineering plants to make their own supplies of the protein resulting in the plant being insect resistant.




Yes, nature does a great deal of chemistry. For us, these chemicals can be a source of good things, a source of good ideas, and sometimes a hazard or problem.


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Why Do Farmers Use Pesticides?

Why do farmers treat their crops with pesticides? The simple answer is because of pests – a wide range of organisms that eat, infect, rot, compete with, or even kill the farmer’s crop. The more complex answer has to do with the nature of pests, with responsibility on the part of farmers, and also with food quality, food waste and food safety.

Pests Are Part Of The Natural Order

Plants in a wilderness area infected with a leaf spotting fungal disease

The same categories of pests that effect crops also occur in even the most pristine, wild environments. Plants are the foundation of the food chain for everything else, and so it makes sense that so many species have evolved to tap into that source of energy. Plants themselves have a variety of ways that they “attempt” to ward off pest damage or competition including the production of pesticidal chemicals. Some of those chemicals are toxic to us as well and need to be inactivated by cooking. We have taken a liking to other plant-made-pesticides like caffeine in coffee or capsaicin in hot peppers. Overall, the reality is that farmer’s crops are attacked by pests is neither surprising nor typically avoidable.


Lateblight UID
Experimental potato plots at Univ. Idaho showing difference between fungicide treated and untreated plants

Pests do not always attack crops to a degree that requires the grower to use a pesticide, but it does often become necessary whether the farm is “Organic” or “Conventional.” When farmers are challenged with potentially damaging levels of pests, it becomes irresponsible not to do something about it. The farmer’s livelihood depends on being able to harvest a sufficient yield to pay for their production costs. There are also only finite supplies of the land and water needed for crop production. Keeping pest damage to low levels is critical for the responsible, efficient use of those resources. Farming also involved inputs like fertilizers, fuel to power tractors etc – also resources that deserve efficient use. High levels of pest infestation and damage are also problematic for the comfort and livelihoods of those who do the key farm labor tasks that feed the rest of us. Finally, if pest damage reduces crop productivity, that can translate into higher prices for consumers – something that is socially undesirable, particularly for families with limited financial resources. There are several reasons why controlling pests is the responsible thing to do for both organic and conventional farmers.

Food Quality and Food Waste

Wormy corn

Sometimes pest damage is dramatically “yucky” from a consumer point of view. For instance, no one enjoys finding worms eating away in an ear of corn or in an apple. No on wants to see maggots crawl out of their blueberries or cherries. A piece of fruit that is just beginning to decay can taste terrible. Even fairly low levels of fungal infection can compromise the flavor of wines made from those damaged grapes. Whether crops go directly to consumers or go into a storage facility first, damage from pests that begins in the field can intensify along as the food moves through the system to the consumer, rendering the produce inedible. When farmers are able to limit pest damage in the field, their products are more likely successfully get through the system and to the consumer in good condition, and less likely to end up as food waste.

Food Safety

ISU Aspergillus Corn
Corn infected with Aspergillus flavus which makes the deadly mycotoxin, aflatoxin

Some plant pests create true food safety threats for livestock, pests or human consumers. Certain fungi (often called molds) produce very dangerous “mycotoxins” in commodities that they infect (grains, nuts, dried items…). Often, these toxic infections occur because of insect feeding damage making the control of those pests critical for safety. Certain weeds are poisonous and can injure livestock if they contaminate hay or other animal feeds. Pesticides are key elements in the programs that keep these toxins out of our feed and food supply.


Pests are a real and often unavoidable challenge for farmers of all types. Whether they are farming “conventionally” or under the organic rules, pesticides are one of several methods that growers integrate to manage this threat and protect their investment. To fail to control pests leads to inefficient use of scarce resources, increases food waste, and compromises the quality and safety of the food supply.

So, yes, farmers use pesticides as needed. In the next post I’ll talk about why that can be done safely.