Grains, Beans, Nuts, and Seeds


Grains, beans, nuts and seeds are all seeds. Rich in complex carbohydrates and fiber, they form the base of most healthy food pyramids. Yet grind grain into flour and suddenly you have a dangerous powder called “refined flour” that is supposed to be avoided like the plague. Gluten intolerance, soy, corn, and peanut allergies are on the rise. What’s going on here?

Yes, these foods are all in the same family—they are all seeds.

Grains are the seeds of grasses.  Examples include:  wheat, corn, oats, and rice

Beans are the seeds of legumes.  Examples include:  peas, lentils, soybeans, and chickpeas.

Nuts are the seeds of trees.  Examples include walnuts, hazelnuts, and pecans.

And seeds are…well…seeds.  Examples include sesame seeds, poppy seeds, and sunflower seeds.

Cut any of these things in half and you‘ll find the same basic structure inside.

This is why there is so much confusion about peanuts, cashews, and almonds, which some people struggle to categorize.  Is a peanut a nut or a legume?  Is quinoa a grain or a seed?  Don’t worry—it doesn’t matter—they are all seeds.  End of story.

What are seeds?

A seed is precious to the plant, since it houses the plant’s embryo—the baby plant—and plants have developed very powerful methods to protect it.   Seeds are designed to survive for a very long time in harsh environments, because they have to sit around and wait for what may be a very long time for conditions to be just right to take root and sprout.  They need to be able to resist cold, heat, insects, worms, bacteria, fungi, and seed-eating animals.  In order to protect themselves from all of these dangers, seeds contain a variety of very smart chemicals, many of which have the potential to disrupt the health of unsuspecting humans.

All plants need help dispersing their seeds, because plants can’t move.  Therefore, plants have evolved very clever ways of dispersing their seeds so that they will go forth and multiply.  Some plants grow tasty fruits around their seeds to entice animals to eat them and carry them away.

But what about grass seeds that have no fruit?  Wheat?  Oats?  Rice? Corn?  Grasses rely primarily on wind to disperse their seeds.  Grains do not come wrapped in sweet fruits, since they’re not designed to be eaten. Grains and legumes were not designed with the health of humans and animals in mind, so no special precautions were taken by the plant to minimize damage to our health. In fact, grains are toxic to humans in their raw state.

Are grains (and other seeds) essential in our diet? 

For the 2 million years before agriculture was invented, our hunter-gatherer ancestors likely ate few, if any grains, so they are clearly not essential.  There have been numerous cultures throughout history (the Inuit Eskimo is a good example) who, even well into the 20th century, ate a completely grain-free diet and were healthy.

Are grains (and other seeds) good for us?

The first time that grains and beans made up any significant portion of the human diet was between 5,000 and 10,000 years ago, when agriculture took hold.  Before agriculture, humans were hunter-gatherers who ate animals and a variety of fruits and vegetables, depending on where they lived and the time of year.  From an evolutionary standpoint, that’s not very long, so most of us have not had enough time to adapt to these difficult foods.  Historical and anthropological records tell us that human health around the world declined in various ways after agriculture was born:  most people were shorter, and their bodies showed evidence of mineral deficiencies, malnutrition, and infectious diseases.  Since dairy products were also added to the human diet at around the same time as grains and legumes, it is hard to be sure whether health declined due to seed foods, dairy products, or both.  However, as you’ll see below, all of the health problems that developed after agriculture could easily have been caused by seed food ingredients, whereas it would be theoretically difficult to tie them to dairy food ingredients (see my dairy page).

Why are we told that grains are healthy? 

We are told that we are supposed to eat at least 3 servings of grain per day, and that half of the grains we eat should be whole grains, yet there is no evidence that grains improve health.  So, where does this advice come from?

There are hundreds of studies proclaiming the health benefits of eating whole grains, but the problem is that these studies compare diets rich in whole grains to diets rich in refined grains and sugars.  These studies do show that whole grains are healthier for us than refined grains (flours), but they do not prove that whole grains are healthy.  In order to prove that, you’d have to compare a diet that contains grains to a diet that contains no grains.  Pretty much any whole food is healthier for us than refined carbohydrates, so proving that whole grains beat refined carbohydrates is…well…a piece of cake.  When you think about it, it doesn’t make sense to say that whole grains are healthy but that powdered grains are dangerous…how can the same food be both incredibly good and incredibly evil?

What makes more sense is to think of it like this:  the more refined a grain is, the worse it is for you.  The reason for this is probably that pulverizing the grains into flour releases more of the carbohydrates and other potentially damaging contents lurking inside the kernel.  If we eat grains whole, the tough outer bran coating, or hull, of the grain keeps more of these pesky particles inside the grain.  If we remove the hull by “polishing” the grain (white rice is a good example), there is nothing left to protect our bodies from being exposed to the starches and proteins inside.

Are nuts and seeds healthier than grains and beans? 

I don’t know.

“Paleo” style diets allow nuts and seeds but not grains and beans, because many of our ancestors would likely have been eating nuts and seeds long before the invention of agriculture.   Most nuts and some seeds do not require any processing to be edible, whereas all grains and legumes must be soaked, fermented, and/or thoroughly cooked in order not to cause immediate illness.  Our ancestors have probably been eating nuts and seeds for a lot longer than they have been eating grains and legumes, so even though nuts and seeds contain similarly risky ingredients, it is possible that our genes have learned how to better handle nut and seed compounds because we have been exposed to them for hundreds of thousands of years.  The best theoretical explanation I can think of for why nuts in particular may be healthier than grains, beans, or seeds, is that nuts and seeds are protected by their hard shells and therefore may not need to incorporate as many defensive chemicals in their flesh as naked beans and grains, but I have not been able to find evidence of this possibility in the scientific literature [if you have information that can help to answer this question, please contact me].

Are grains, beans, nuts and seeds nutritious?

Grains are so low in nutritional value that most cereal products in the United States are fortified with vitamins and minerals.

Of the four categories of seed foods, beans are usually thought of as being the most nutritious, due to their high protein content.  As you can see from the nutrition information for cooked pinto beans, they are mostly made of starch (carbohydrate–something the body has no need for), along with some protein, fiber, and some iron.

Yes, there is some protein and some iron in these foods as well.  However, all of these nutrients, because they come from seed foods, come with some baggage, as you’ll see below.


Seed proteins are typically of lower quality due to missing essential amino acids (quinoa and soy are notable exceptions).  For example, wheat protein is particularly low in lysine.  Corn is especially low in tryptophan.  Legumes (including soybeans) are especially low in sulfur-containing amino acids, cysteine and methionine.

Some of the proteins in seeds are naturally difficult for us to digest because of their special structure.

Some seed proteins are defensive molecules that are designed to irritate non-plant cells.


The outer coatings of seeds are armed with proteins called lectins (aka phytohemagglutinins, or agglutinins), which are part of the plant’s immune system.  Lectins can recognize friend from foe by reading carbohydrates on the surfaces of the cells of would-be invaders.   When a seed is stressed or damaged, lectins are released to identify and attack potential enemies.  One of the many ways they can fend off an attack is to zero in on targets (such as bacteria), bind to their signature carbohydrates, and then cause them to clump together (agglutination) so they cannot advance.  Insects, not people, are the natural predators of grains, so lectins can also cause infertility in insects.

Lectins are found in all plants and animals, not just in beans and grains.  However, animal lectins and plant lectins are different; animal lectins are not known to harm the cells of other animals, whereas plant lectins can be risky for humans and other animals.  The highest concentrations of the most potent plant lectins are found in the seeds, roots, young shoots, and bark of plants.  In seeds, lectins are primarily found in the bran-rich outer coating, which is one reason why even whole grains are not necessarily healthy. Lectins can also be found in the oils of seeds and nuts.  The most important food sources of lectins are grains, beans, nuts, seeds, tomatoes, white potatoes, limes, cinnamon, and Jerusalem artichokes.

What can lectins do to humans?

Lectins, because they bind to specific carbohydrates on the surfaces of living cells, are very reactive.  You can think of them as being sticky.

Lectins can bind to glycoproteins on the surface of our intestinal cells.  Lectins have been shown in laboratory studies (in vitro) to damage human intestinal cells and in animal studies to poke holes in their intestinal linings, causing increased intestinal permeability (leaky gut). Leaky gut syndromes in humans have been associated with autoimmune diseases such as:  rheumatoid arthritis, Celiac disease, type I diabetes, and multiple sclerosis.

We know that lectins cross into our bloodstream because healthy people have antibodies to lectins in their blood. In the bloodstream, lectins can bind to red blood cells, causing them to clump together (or “agglutinate”).  Clumped blood cells are then destroyed by the body, so high doses of lectins can cause anemia.

Lectins can also bind to our immune cells and cause them to clump together, weakening our immune system.  However, lectins can also bind to immune cells (mast cells and T cells) and activate them; this is a potential path to allergies and autoimmune diseases. They can also trigger white blood cells to release pro-inflammatory cytokines.

Lectins can enter cells, and once inside, they can bind to and inactivate ribosomes, which are the tiny protein factories inside of our cells.

In laboratory science, lectins are well-known as “mitogens”—which means that they can cause cells to multiply in a cancerous fashion.  In laboratory studies, lectins can bind to immune cells called lymphocytes (T cells in particular) and trigger cancerous changes.  In clinical human studies, ingestion of peanuts has been shown to have the ability to cause cancerous proliferation of colon cells.

How to reduce the lectin content of foods

Most lectins can be completely inactivated by pre-soaking foods and then bringing them to a full boil for 15 minutes.  Dry heat (baking or roasting) is not as effective as prolonged boiling, so baked goods made with grain or bean flours are not as safe as boiled products. Dry roasting only removes about 75% of the lectins from raw peanuts.  Toasted wheat germ contains active lectins, as well.  Lectins laugh at stomach acid, and many lectins resist digestion by our intestinal enzymes.  Lectins are the reason why grains and beans should never be eaten raw (kidney bean lectin is very toxic if eaten raw or undercooked, and will cause severe vomiting).

Sprouting reduces (but does not eliminate) lectins because once the seed starts to germinate and form a baby plant, much of the lectin protein gets broken down to nourish the growing seedling.  However, some lectins remain to protect the growing plant.

Thus, there are really only two ways to protect yourself from the many potential hazards of lectins:  prolonged boiling or avoidance.

There are many different types of lectins, with different carbohydrate targets, attack strategies, and potencies.  The best-studied of the food lectins are:  wheat germ agglutinin, peanut lectin, kidney bean lectin, soybean lectins, potato lectin and tomato lectin.  In the future I will be writing more about these foods and their specific lectins.


What is gluten? 

Gluten is not a single protein; there are hundreds of proteins in the gluten family. Glutens are proteins found only in the following grains:

  • Wheat (bulgur, durum, farina, graham, kamut, matzah, seitan, semolina, spelt)
  • Barley (malt)
  • Rye
  • Triticale

[Oat crops are often rotated or milled with wheat products, so oats are sometimes cross-contaminated with wheat glutens.] 

Glutens are simply seed storage proteins—they are designed to nourish the plant embryo when it comes time to sprout.  Sounds innocent enough…yet, glutens are not only the well-established cause of Celiac disease, a serious autoimmune condition affecting more than 1 in 100 people, but are also the cause of gluten sensitivity, which affects (probably many more than) 7 in 100 people.

Glutens and other storage proteins are found on the inside of all seed foods (in the endosperm), not in the bran-rich outer coating, which is probably why refined (powdered) grains are potentially less healthy than whole grains.  All seeds contain storage proteins, but only the wheat family contains glutens.  So, what’s so special about gluten?

Glutens contain stretches of repetitive amino acid sequences (rich in proline and glutamine) that are particularly difficult for our enzymes to digest.  [Remember, the mother plant does not want this protein to be digested by anyone else other than the baby plant.]  Proteins that contain proline-rich sequences are called “prolamins”, and they are thought to be particularly irritating to our immune systems.  All grains contain prolamins, but the types found in wheat (gliadin), rye (secalin), and barley (horedin), seem to be particularly irritating to the immune systems of susceptible individuals.  [A small number of people are also sensitive to avenin, the prolamin found in oats.]

The problem with gluten being poorly digestible is not just that we have a hard time extracting nutritious proteins from gluten-rich foods.  The problem is that partially digested glutens, which are called “toxic gliadin peptides”, can wreak havoc with the digestive and immune systems of genetically susceptible individuals, leading to gluten sensitivity and Celiac disease.

Wheat Allergy

People who are have a true allergy to wheat are reacting to a specific wheat protein called omega-5 gliadin.  This protein is only found in wheat—not in barley, rye, or triticale.  

Seed “Antinutrients” 

An “antinutrient” is anything that interferes with the ability of the body to digest, absorb, or utilize a nutrient.  Antinutrients in seed foods include enzyme inhibitors and phytic acid.

Enzyme Inhibitors

Seed foods contain compounds that work against our digestive enzymes, making it harder for us to break foods down.  These include protease inhibitors, which block protein digestion, and amylase inhibitors, which block starch digestion.  Amylase inhibitors do not survive digestion, so they are not a concern.  Protease inhibitors are mostly destroyed by cooking, so, in well-cooked seed foods, these would also not be a problem.

Phytic Acid

Phytic acid, however, cannot be destroyed by cooking.  The name phytic acid essentially means “plant acid” and was so named because it is not found in animal foods.  It is located primarily in the bran-rich outer coating of seeds, which is one reason why even whole grains are not necessarily healthy.

Phytic acid is a mineral magnet.  It binds to certain minerals in the foods we eat, and removes them from our bodies.  This can lead to mineral deficiencies, such as iron deficiency anemia.  [The form of iron found in plant foods is difficult to absorb to begin with, because it is in the “non-heme” form, instead of the “heme” form found in animal foods.]

Below are results from an experiment showing that bran blocks the absorption of about 90% of the iron in wheat rolls, both in omnivores and in long-time vegetarians.  This demonstrates that, even in people who have been eating high-plant diets for years, the body does not adapt to the antinutrient effects of phytic acid:

[Brune et al 1989]


*Taking vitamin C or eating vitamin C-rich foods along with high-phytate foods can improve mineral absorption.

Phytic acid is best at binding to “positively charged, multivalent cations”, which means that it prefers minerals with more than one positive charge, such as iron (Fe+2), calcium (Ca+2), Zinc (Zn+2), Magnesium (Mg+2) and Copper (Cu+2), which are all essential minerals that we must obtain from our diet.  [It is not good at binding minerals like sodium (Na+1) or potassium (K+1), which have only one positive charge.]

Phytic acid can also bind to food proteins and to our digestive enzymes, interfering with protein absorption.

Which foods are highest in phytic acid?

Phytic acid is found in all parts of plants, and therefore is found in all plant foods; however, the vast majority of it is located in seeds, where its job is to hold on tightly to the essential minerals (phosphorus, iron, zinc, etc.) that the baby plant will need to grow.  Once the seed begins to sprout, phytic acid gets broken down so that those vital minerals can be released to the baby plant. This is why non-seed parts of the plant contain extremely low concentrations of phytic acid.

The amount of phytic acid in any given seed food varies tremendously, depending on a variety of factors—environmental conditions, age, plant variety, etc, so it’s hard to say, but some research indicates that seeds contain highest levels, followed by grains, and then legumes.  The phytic acid content of nuts runs the gamut from low to high.

How to reduce phytic acid content

Most phytic acid is not digested; it survives our stomach acid and our intestinal enzymes, making it all the way down into the colon, where bacteria can start to break it down.  Phytic acid does not appear to be absorbed by our systems, so it can only interfere with minerals in our digestive tract, not in our bloodstream or inside of our cells.  Most phytic acid leaves our system intact, carrying minerals away with it.

Phytic acid is not affected by prolonged storage. Phytic acid cannot be destroyed by cooking, not even with prolonged boiling.  Extrusion cooking, which is used by manufacturers in the industrial production of breakfast cereals, for example, barely reduces phytic acid content.

Phytic acid might be partially reduced by soaking and/or sprouting.  For example, when performed properly, under just the right conditions, between 1/3 to 2/3 of phytic acid can be removed from beans.

Fermentation, particularly sourdough fermentation, is the most effective method for removing phytic acid from foods, because microorganisms, unlike humans, have the ability to digest phytic acid.

Seed Starches

Plants store energy as starch, which is just a bunch of simple sugar molecules linked together.  Seeds are very high in starch because the baby plant will need a source of energy when it starts growing.

Much of the starch inside seeds is either amylose or amylopectin, which are both made of long chains of glucose molecules, and therefore easily broken down into glucose and absorbed as glucose into the bloodstream.  However, there are two types of seed carbohydrates that our digestive enzymes can’t break down:

  • Fructo-oligosaccharides (chains of fructose molecules) 
  • Galacto-oligosaccharides (chains of galactose + glucose + fructose).  Examples include raffinose and stachyose. 

Beans, beans, the wonderful fruit…

Most seed foods contain some combination of the indigestible carbohydrates listed above, but beans are best known for causing digestive problems.  This is because legumes are especially high in the galacto-oligosaccharides stachyose and raffinose. 

Bacteria living in the colon make an enzyme called “alpha-galactosidase” which can break apart the sugar molecules in these carbohydrates.  Then the bacteria proceed to ferment those sugars, creating unwelcome gases:  carbon dioxide, hydrogen, and/or methane.   Beano® contains the same enzyme that bacteria use.  By swallowing Beano® before eating beans, raffinose and stachyose will get broken down into sugars long before reaching the colon, so the small intestine can absorb the sugars before the bacteria can get to them.

Of note, rice is extremely low in indigestible carbohydrates, and therefore very little gas is produced during its digestion. Spelt is also quite low in these substances.

Cyanogenic Glycosides 

These innocent chemicals are mainly found lurking deep inside the rugged pits of fruits, such as apricots, peaches, cherries, mangoes, and plums.  These types of seeds are virtually indestructible without tools, and it’s a good thing we can’t chew them open.  When these seeds are damaged, the nontoxic glycosides mix with an activating enzyme and poof—you’ve got cyanide.  Other foods that can generate cyanide include:  bitter almonds, marzipan, bamboo shoots, cassava root (tapioca), lima beans, sorghum, apple seeds and pear seeds.  Proper processing of these foods by grinding, boiling and soaking can remove the cyanide and make them safe to eat.

The human body can detoxify tiny quantities of cyanide, but at higher doses, cyanide can interfere with iodine within your thyroid gland and cause goiter or hypothyroidism.  At higher doses still, cyanide can suffocate your mitochondria (your cells’ energy generators), which can be fatal.

Bottom line about seed foods

Of all natural plant and animal foods available to humans, seed foods are the foods most likely to endanger human health.  Therefore, eliminating foods from this family is the single most important dietary change you can make to improve and protect your health.

For people who either choose not to eat animal foods, or do not have access to animal foods, this food group does contain the highest amounts of protein of all of the plant foods, and can be a far less expensive source of protein than meat and dairy products.


  • these proteins can be difficult to digest, partly due to their nature and partly due to anti-nutrients within these foods
  • certain proteins, such as gluten, can be particularly irritating to the digestive tract and immune system of susceptible individuals
  • lectins within seed foods are potentially hazardous, making boiling or steaming to remove these risky substances before consumption very important.

Some of the starches in seed foods cannot be digested by our intestinal enzymes, therefore they ferment in the colon, creating gases.

The mineral thief phytic acid is very difficult to completely remove from these foods, even with fermentation techniques, therefore these foods significantly increase the risk for mineral deficiencies, especially iron deficiency and associated anemia. Taking Vitamin C can improve the absorption of iron.

If you choose to eat seed foods such as grains, it is best to eat them whole, rather than ground into refined flours.

Rice may be safer and more comfortable to eat than other grains because it

  • does not contain gluten
  • is extremely low in indigestible starches
  • is typically boiled (or steamed) before eaten, which destroys all lectins

It is unclear to me whether nuts and seeds are healthier than grains and legumes.

Sign up to be notified of my latest posts!

Signup now and receive an email once I publish new content.

I agree to have my personal information transfered to MailChimp ( more information )

I will never give away, trade or sell your name or email address. You can unsubscribe at any time.


Biesiekierski JR et al. Quantification of fructans, galacto-oligosacharides and other short-chain carbohydrates in processed grains and cereals. J Hum Nutr Diet 24: 154–176.
Brady PG et al. Identification of the dietary lectin, wheat germ agglutinin, in human intestinal contents. Gastroenterology 1978; 75(2): 236-9.
Brune M et al. No intestinal adaptation to a high-phytate diet. American Journal of Clinical Nutrition 1989; 49: 542-545.
Cummings JH and Stephen AM. Carbohydrate terminology and classification. European Journal of Clinical Nutrition 2007; 61(Suppl 1): S5-S18.
Dalla Pellegrina C et al. Effects of wheat germ agglutinin on human gastrointestinal epithelium: insights from an experimental model of immune/epithelial cell interaction. Toxicology and Applied Pharmacology 2009; 237(2): 146-153.
DeHoff PL et al. Plant lectins: the ties that bind in root symbiosis and plant defense. Mol Genet Genomics 2009; 282(1): 1-15.
Fassano A. Leaky gut and autoimmune diseases. Clinic Rev Allerg Immunol 2012; 42: 71-78.
Goodman AH et al. The chronological distribution of enamel hypoplasias from prehistoric Dickson Mounds populations. American Journal of Physical Anthropology 1984; 65: 259-266.
Lajolo FM and Genovese MI. Nutritional significance of lectins and enzyme inhibitors from legumes. J Agric Food Chem 2002; 50: 6592-6598.
Mummert A et al. Stature and robusticity during the agricultural transition: evidence from the bioarchaeological record. Economics and Human Biology 2011; 9: 284-301.
Nachbar MS and Oppenheim JD. Lectins in the United States diet: a survey of lectins in commonly consumed foods and a review of the literature. American Journal of Clinical Nutrition 1980; 33: 2338-2345.
Ovelgonne JH et al. Decreased levels of heat shock proteins in gut epithelial cells after exposure to plant lectins. Gut 2000; 46: 679-687.
Pietzak M. Celiac disease, wheat allergy, and gluten sensitivity : when gluten free is not a fad. J Parenter Enteral Nutr 2012; 36: 68S-75S.
Pusztai A and Grant G. Assessment of lectin inactivation by heat and digestion. Methods Mol Med 1998; 9: 505-14.
Pusztai A et al. Antinutritive effects of wheat-germ agglutinin and other N-acetylglucosamine-specific lectins. British Journal of Nutrition 1993; 70(1): 313-321.
Ramadass B et al. Sucrose co-administration reduces the toxic effect of lectin on gut permeability and intestinal bacterial colonization. Dig Dis Sci 2010; 55(10): 2778-84.
Rhodes JM et al. Lectin–epithelial interactions in the human colon. Biochemical Society Transactions 2008; 36(6), part6: 1482-1486.
Ryder S. Peanut ingestion increases rectal proliferation in individuals with mucosal expression of peanut lectin receptor. Gastroenterology 1998; 114(1): 44-49.
Schlemmer U et al. Phytate in foods and significance for humans: food sources, intake, processing, bioavailability, protective role and analysis. Mol Nutr Food Res 2009; 53: S330-S375.
Sollid LM and Jabri B. Celiac disease and transglutaminase 2: a model for posttranslational modification of antigens and HLA association in the pathogenesis of autoimmune disorders. Current Opinion in Immunology 2011; 23(6): 732-738.
Thcernychev B and Wilcheck M. Natural human antibodies to dietary lectins. FEBS Letters 1996; 397(2-3): 139-142.
Last Modified: Sep 13, 2015