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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How Can Pesticides Be Safe?

Many people may find it difficult to imagine how a pesticide could ever be safe. To understand how that is possible, it is helpful to make the comparison with something more familiar: electricity.

It is hard to envision modern life without electricity. As much as we enjoy and need this source of energy, it involves some hazards. Electricity can, and sometimes does, cause injury or death.  Yet overall, we think of using electricity as a reasonably safe aspect of our lives.

Safety can’t be precisely defined. What we perceive as safe is something where the benefits more than offset the minimal risks. We can enjoy electricity’s benefits with little risk through two main strategies: 1) using low-hazard forms of electricity and 2) keeping ourselves from being exposed to hazardous forms of electricity.


The Low-Hazard Approach

Increasingly, we power the devices central to our lifestyles with forms of electricity that are practically non-hazardous. The prime examples would be our cell phones, Bluetooth devices, or portable music players that run on low-voltage, direct current electricity which is nearly incapable of causing us harm.  That same, low-hazard approach plays an important role in pesticide safety.

In the middle of the last century, a number of the early pesticides in use were chemicals that were quite toxic to mammals, and thus to humans. The U.S. began to seriously address the issue with the establishment of the U.S. Environmental Protection Agency (EPA) in 1970. Soon, the truly dangerous pesticides were removed from the market or their use was greatly restricted.

Since then, billions of dollars have been spent on the discovery, testing and regulatory review of new, far less toxic pesticide options. In the charts below, I’ve examined the toxicity of crop protection materials that have been used through looking at historical U.S. Department of Agriculture (USDA) data on Washington State apples and California pesticide reporting data from all crops in 2013. In these charts, the toxicity is based on feeding studies with rats or mice, which is used as an indicator of potential toxicity to humans. Other measures of toxicity have similar trends.


The EPA has four toxicity categories to classify the acute hazards of pesticide products. For use in apple orchards, the data show that pesticides from EPA Category I, Highly Toxic, were never more than 10% of the total pesticides used, and that their use has steadily declined. These would be pesticides as toxic as the nicotine that is sold for e-cigarettes. Only 0.2% of the pesticides applied to California crops in 2013 were in this category.



EPA Category II, Moderately Toxic, includes materials with toxicity in the same range as the capsaicin in hot peppers or the caffeine in coffee – familiar and even sought-after natural chemicals in our diets. That category represents very limited use on apples today, and only 18% of what growers applied in California apple orchards in 2013.

The pesticide use category that has grown is termed Slightly Toxic (EPA Category III). Toxicity for crop protection materials in this category is in the same range as the citric acid in a lemon or the vanillin in a vanilla bean.

The largest category of pesticides applied to apples and other crops today is Practically Non-Toxic for mammalian consumption (EPA Category IV). Comparing this to our use of electricity, we can see that low hazard is a major strategy through which we minimize pesticide risk.

To understand how something that is designed to kill or otherwise control a pest could be non-hazardous, consider the example of chocolate which has a flavor ingredient that we humans love but which can be toxic to our pet dogs. Chemicals can have different effects on different species. Scientists use the terms specificity and mode of action to describe how chemicals have their specific effects. With modern pesticides, the mode of action is normally the inhibition of some specific enzyme that is important to the viability of the pest. If the enzyme is inhibited by the pesticide, the pest might stop eating, stop growing and/or die.

That enzyme often isn’t one that even exists in humans and other animals ourselves or in other groups of organisms unlike the pest. A modern insecticide usually only affects enzymes that are found in insects or even a few kinds of insects. A modern herbicide might only inhibit an enzyme that is needed for the growth of plants. A modern fungicide inhibits an enzyme in a pathway of enzymes that is found in certain fungi. While all of these products should still be handled with a reasonable degree of caution, they are, like the electricity that powers our cell phones, low hazard and thus low risk. We can feel safe about their use.

Limiting Exposure Risk When There Is a Hazard

We still need the more hazardous forms of electricity (such as the 120 volt alternating current) for needs like lighting, heat, air conditioning etc. To minimize risk, we’ve developed safe guards such as systems of insulated wiring, childproof plugs, circuit breakers and GFCI outlets to keep us from being exposed to that hazard. Where we need 220 volt service, we have even more ways to avoid exposure. To be connected to the grid we need the extremely hazardous, high-voltage electricity coming to us from wherever it is generated. The high-power transmission lines are designed to make it unlikely that anyone will be exposed to that extremely hazardous form of electricity.

Some pesticides that we need to manage certain pests represent a possible hazard to mammals, like humans, or sometimes to other non-target organisms like birds, fish amphibians or aquatic invertebrates. The safe use of these pesticides is all about limiting exposure. For all pesticides used in agriculture, anyone who is directly involved in the mixing or application of the chemical must follow specific requirements regarding protective clothing and equipment. For low-hazard materials, that might just be gloves, closed shoes and a dust mask. For something that could be a significant human hazard, those restrictions would include a respirator and a protective whole-body TYVEC™ suit.

Restrictions can also dictate how soon after an application anyone can re-enter a treated field (re-entry interval or REI). For low-hazard pesticides, that time period can be a few hours or less. For more hazardous pesticides, the REI can be a number of days. For pesticides that are hazardous to fish or other aquatic organisms, restrictions mandate how close applicators can apply them to waterways. Similarly, for pesticides that are hazardous to bees or other pollinators, restrictions control when applicators can apply them relative to bloom times and/or times of the day when bees and other pollinators are working.

For all pesticides, the EPA conducts an extensive risk assessment and uses that information to set up a detailed set of restrictions designed to prevent the existence of any residues of concern to consumers by the time the crop is harvested. The details of this system are discussed in another post titled, Do I Need to be Concerned about Pesticide Residues on and in My Food?

The moral of this story: just like electricity, pesticides can be used in a way that meets our need for clean, productive farming while giving us a comfortable and functional level of safety.