Investigation: Genetically Modified Organisms

The purpose of this blog is to take the products of science, especially those which we encounter in everyday life, and explain the actual facts of them in plain English.  To that end, I can't think of a more appropriate, or more timely, topic to discuss than genetically modified organisms (GMOs).

Public domain image, courtesy of USDA ARS.

When I started this blog, I had an eye on doing a series on GMOs.  Recently, I've joined an effort by a
national non-profit organization to help its members understand agricultural issues, and GMO crop plants are part of that.  So it's time to explain them, in all their complexity: what they actually are, how they're created, what plants we're looking at, testing, regulation, health and environmental concerns, the whole shebang.

There's so much emotional investment in this topic -- nothing hits closer to home than food, water, or shelter -- that it's particularly important to drill down to real facts, on all sides, and answer as many of the nagging questions as possible.  These articles will be, to the best of my ability, impartial.  All that this series assumes is that major governments are not out to poison their people, the scientific process and community are (on the whole) to be trusted, and that there really are hard, solid facts to build conclusions from.  If you're willing to grant those points, let's go ahead with a rational investigation.

The Series
As each piece is completed, I will post a link to it here; bookmark this post to serve as an index.  More will be added as I complete the initial research and figure out how to group upcoming topics.

Definitions
Methods (and a peek into genetics)
Plants and other organisms
Genes
Testing and regulation
Market share, availability, and restrictions
Concerns
Potential benefits and drawbacks
Afterword

I have a full segment planned on specific questions and concerns, especially about health and environmental risks, where I will address them in Q&A format.  If you have a specific concern that you'd like me to address, please tell me, and I'll add it to the list if it isn't already there.

Thanks for reading, and stay tuned.

[Editorial] On Science

I'm about to embark on a major project for this blog, but before I do, I thought I should touch on science itself: its role, and its responsibilities.

Public domain image, courtesy of Adorable Wallpaper

I'm a scientist.  I say that not because I do academic research (I don't), or because I hold degrees in some branch of science (I do), or because I work for a company doing scientific R&D (again, not the case).  I call myself a scientist because I believe science is a powerful tool that can be applied to many parts of our lives, and a means to answering many questions (some of which have real and immediate impact).  I call myself a scientist because I use science nearly every day, on a personal level.

Science is a process.  You don't need a lab or even a formal education to use it; the only special equipment required is a brain.  It is a process of observation, analysis, projection, and deduction which makes sense of the world around us.  That's all.  Like any tool, you need to understand how it works, and use it properly, to get a good result, but when you get down to the process itself, it's not complicated.

The first step is to find something you want to know about.  It might come about from seeing something in your backyard and thinking, "That's odd.  Why is this happening?"  You look a little closer, and observe it.  You ask somebody who might know a little about it.  Then, from what you see and hear about it, you form an idea.  "This must be why it's happening."  Many people stop there, and go on to other things.

Science takes it further.  You figure out a test which would show whether you're right or not.  "If that's why it's happening, then this other thing must be going on."  You try to gather more observations to show that your deduction, your hypothesis, is right.  If you can't support it, then you can't say that you were right in the first place (but you might not be wrong).  If the evidence does back you up, then you can conclude that your original idea is correct.  If a bunch of different tests still show you were right, you can say you've proven a theory.  It's backed up by facts, and it's as solid as all your tests can make it.

We talk loosely about the laws of physics, but science doesn't actually have "laws", it has theories.  Unlike a guess that you might make offhand, some of those scientific theories are supported by so much evidence, and so many tests, that they're about as close as you can get to law.  Theories aren't set in stone, though: they can be disproven.  Someone can always challenge a theory.  Keep in mind the word "disproven" -- to take down a proven theory, it must be proven wrong in a manner equally convincing.

This is the heart of the tug-of-war at the heart of the scientific community.  People are always making new theories, and their fellows are pulling the theories this way and that, trying to show any holes or see whether they'll come apart.  Old, established theories have new experiments picking away at them, to find out whether there are cracks in them in the light of what we know now.  It's dynamic, sometimes chaotic, often full of arguments, but out of that process -- the scientific method and the discussions that follow -- comes a robust understanding of how the world works.

There is such a thing as bad science, where the process isn't applied correctly.  When you only accept evidence which says you're right, that's bad science.  Using the wrong equipment, or limiting yourself to small groups or places, can bring in errors that lead to bad conclusions.  To get the sort of solid, reliable results that you can depend on like fact, the tool of science has to be used properly, from beginning to end.  Making sure of that takes more than having a couple of other scientists look over what you did, which is what "peer reviewed" means.  It takes getting what you did out there, into the scientific community, so that everybody can see it and decide whether you did it right.  Only by that sort of teamwork can science build on our knowledge.

There are those who say that science is a kind of religion, that scientists have faith in science like a Christian has faith in God.  That's not really true.  We have confidence in science.  We have trust in science.  One difference between trust and faith is that a subject must prove that it is worthy of trust to earn it, but must prove itself unworthy of faith to lose it. It's a question of on which side of the line the burden lies.

The fact that trust is so easily lost is why scandals about the scientific community can be so damaging.  Finding out that a prominent scientist falsified his data, or that the authors of a published paper don't actually exist at all, make us wonder about all the other scientists and papers out there.  It throws doubt on the whole field of science.   It's fair to ask, "Did this person use the evidence they gathered properly?"  It's good to wonder whether the way we accept formal papers and seek consensus is useful.  What we shouldn't fall into is a doubt of the scientific method itself.  

Science is a tool, one which has proven its usefulness time after time.  If something goes wrong, it's not the tool that's at fault -- it's the person using it.  We all make mistakes, and there are people who will try to deceive others; the tug-of-war in scientific discussion is how we find those out and expose them.  The community as a whole wants to find the truth, which is the ultimate goal.  What one person wants, or wishes, has to give way to that.

As a scientist, I want to find the truth, as best we can understand it.  As someone who writes about science, I strive to stay impartial, and set aside my own biases in the pursuit of that truth.  I do have very strong feelings about some issues, but those feelings have no place here, except as a driving force.  What I put here, on this blog, is my best effort to distill facts into a form everyone can understand, without opinion.  I take pride in doing it well.  The sole exception is in pieces like this editorial, which are my own thoughts, lacking the usual references. I promise these editorials will be well-labeled.

As you read about the science I explore here, ask questions.  "Where did she get that?"  "Is that really what happens?"  Challenge what you read.  Check up on it.  I offer references; if you can find evidence that says my conclusion is wrong, call me on it.  All I ask is that you use the most fundamental evidence you can, from what is called "primary sources": research papers, government figures, impartial investigators without an axe to grind.  I drill down to primary sources for my conclusions; to make a convincing argument, you'll need to do likewise.  If you do that, I promise not to be offended if you tell me I'm wrong.  (Just be ready for me to come back with why I might still think I'm right.)

Always think, question, analyze, challenge.  It's what makes us strong.

What's this "GMO Protection Act" thing?

This is not quite so much "hard science" as the intersection of plant science, law, and policy.  It can still be dressed in street clothes, though, so bear with me here.

Sugar beet harvest
(Creative Commons, courtesy of Katy Walters)

Right now (April 2013) there's a lot of buzz about a piece of law¹ added into the Agricultural Appropriations Bill that just passed.  Various news outlets have been drawing conclusions about who masterminded it, who benefits, and what it does to consumers.  I'll leave it to journalists to explain when and how it got there (hopefully with some actual journalistic integrity); I'm here to explain what the heck it is, based only on a reading of the law itself plus a little recent history.  It does have implications for who decides what makes it to your plate, and how -- but those impacts are nowhere near as major as some of the headlines make it sound.

I'm not a lawyer, of course, but I can read pretty twisty stuff -- the scientific papers I had to decipher in grad school were pretty good training material.  It's the same principle, really.  I'll include the text after my own summary and analysis, in case you want to try your hand.

Summary: The US Department of Agriculture (USDA) has decided that genetically modified organisms (GMOs) should be legally classified as "plant pests"², because the modification is done by a bacteria which normally causes disease in plants, and the plant and bacteria are inseparable from that point (or something to that effect). To be grown commercially, a GMO has to be studied and determined not to be a pest. None of this applies to plants produced by traditional breeding programs, just those which have been modified by inserting genes in laboratory conditions.

So, this law says: if someone declares that a particular GMO deserves to have its "not a pest" status taken away, the Agriculture Secretary has to investigate, and also has to grant requests for temporary exceptions to farmers who request them, regardless of what any other law says about it.  Those temporary exceptions include shipping, planting, growing, selling, and so on.  The Secretary can impose measures to lessen environmental effects, assuming the growers can carry on their business in a timely manner.  Those exceptions stand until the Secretary makes a decision whether the GMO really is a problem.  That decision "shall be based on sound science".  That's what just got passed.¹

Note: This applies to the Agriculture Department's plant pest regulations, not public health regulations.  Section 411 of the Plant Protection Act handles plants which constitute a risk to other plants, not to human or animal health. So this little end-run around court orders doesn't apply if that order is based on a perceived risk to people, rather than the environment or other crops.  The Plant Protection Act does not distinguish between crop plants and surrounding plants, so threats to things growing outside a field presumably qualify.


Example: Someone says that the environmental assessment for genetically-modified Crop X failed to investigate damage to a native wildflower.  It goes under review (again) by the Agriculture Department, which approved it the first time.  In the meantime, a commercial farmer can petition to sow Crop X on schedule, so that if it's decided that the plant is okay in the end, he won't have lost one or more growing seasons waiting to find out.  Additionally, if the person with the complaint convinces a judge that it's so much of a risk to the environment that all the fields of Crop X have to be ripped out, the exception granted by the Agriculture Secretary overrides that court order, until the Secretary makes his/her decision.

From an environmental protectionist standpoint, this is bad.  You can come forward and make your case against Crop X, and even if you get a court order to stop growers from planting it, and to pull up all fields of Crop X currently planted, the Agriculture Secretary can (must) grant an exception to anyone who wants one.  The Agriculture Secretary can require that growers take steps to make sure the pollen/seeds/whatever from the GMO doesn't come in contact with known wildflower habitats, but the growers can otherwise go ahead as usual.  Meanwhile, you're watching flower populations anxiously and waiting for the Agriculture Department to come around. If the endangered plant is an open-pollinated variety of the same crop plant, it would have organic and heritage farmers up in arms as well.

From a grower's point of view, it's a relief.  In 2010, this scenario came up², and a judge ordered all of the GMO sugar beets ripped out of the ground, because the approval of five years back was challenged. The growers involved would have lost quite a bit of money, and it was all reversed some months later, when the sugar beets were once again granted non-pest status by the Agriculture Department. If a question is raised about a crop you're about to sow, you might hold off on sowing it; if that goes on long enough, you could lose your income for a season, maybe more. If it happens with something you have in the ground, like alfalfa, you could have to till under a crop which was supposed to produce for several years. Most growers are not flexible enough to switch types of crop easily, and there aren't many varieties available for conventional farming in some crops, like sugar beets or soybean.

So is it something to be concerned about? As always, that depends on your priorities. It does limit the court's ability to determine whether growers can produce a given GMO in the face of challenges to its environmental safety or impacts on other crops. Those limits were in response to previous cases where those growers lost significant income because of challenges which were later reversed.  Knowing that background, you are free to make an educated decision.


And now: jargon ho, look out below (the cut)!

What do plant roots take from the soil?

This is a pretty complex and wide-reaching question, and I've run across it in many forms. From "Does adding sugar to the soil make tomatoes sweeter?" to "Do antibiotic residues in chicken manure end up in my lettuce?", what plants assimilate from the soil is a significant issue for many.

From basic plant biology, we know that plant roots pull several things from the soil they grow in: water, simple ions like nitrate (the major source of nitrogen), and mineral ions like magnesium and calcium. (Ions are charged molecules, carrying a positive or negative charge like one post on a battery.) These are used as building blocks for growth. They're all small molecules, usually readily dissolved in water, with the exception of a few minerals. Few biology courses go beyond that.

Plants don't just suck up everything randomly, though. Roots are highly evolved organs, serving as the gatekeepers for what gets into the plant's circulation. The anatomy of a root varies depending on its age and the type of plant, but the basic structure of an active root is in rings: an outer fleshy part which is able to absorb whatever's around it, an inner core where the circulatory tissue is, and in between, a ring of cells with an impermeable "mortar" cementing them together. That mortar, called the Casparian strip, is what ensures that anything going into the plant's circulation has to go through one of those guardian cells.

They're picky, too. They only let in a certain amount of water, to keep the interiors of the other cells from getting too diluted. They pay attention to the concentration of ions like iron, magnesium, and potassium, and actively manage their uptake. There are specific gates in the cell membrane for several things, and lots of other molecules get left out.

By the nature of those membranes, some types of molecules can just walk right in, however. Cell membranes are mostly made up of oily compounds called lipids, which glob together to make a fatty bubble, dividing the water inside the cell from the water outside the cell. Molecules which resemble those lipids can sometimes sort of phase right through, like a pedestrian making his way across a line of people. He bumps, and jostles, and comes out the other side. A repeat performance on the other side of the cell, and they're into the part of the root where they can enter circulation.

In some cases, plants will intentionally take up things which they don't actually need, for one reason or another.  Many studies have been made of plants which can take up excess minerals, called hyperaccumulators; one such plant managed to accumulate enough nickel to make up a quarter of its sap.¹  And food scientists have known for years that rice is very good at accumulating arsenic, to the point that rice from the southeast United States can have significant amounts of it, when grown in old cotton fields where arsenic-related pesticides were once used.²  The reason rice takes up arsenic, even though it's not needed for growth, is that it closely resembles silicon -- and rice uses a lot of silicon, in its common form of sand, to make sturdy stems and leaves.  The gates can't tell the difference, so they pull both in.

To take it one step further, bioremediation is the process of using plants to decontaminate soil; beyond taking up simple elements as mentioned above, some plants can accumulate, break down, or attract microbes that eat more complex hazardous materials like PCBs.³  Plants that naturally take up compounds like that are rare, and often have to be specifically engineered for that purpose.

So the quick answer to "Does X make it from the soil into my food?" is... it depends on what X is like. If it's a small ion like those in table salt, it'll only get taken up if the plant wants it. If it's a larger, but still highly water-soluble chemical like white sugar, it's even less likely. The compounds which are most likely to cruise through the gatekeepers and end up in the rest of the plant are slightly oily, smallish molecules that aren't too afraid of water.^4,5

There's a lot of those, including ones that are used as pesticides, some antibiotics, and others that are considered hazardous soil contaminants.  So it's important to know whether they actually make it into what we're eating.  Unfortunately (you saw this coming) it's not simple to figure that out.

Take an antibiotic used in animal feed.  In order to end up in your green salad, it has to travel a long way: from the animal feed, through the animal, into the manure, through manure storage and handling, onto (or into) the soil, into the plant root, through the plant's circulatory system, and finally coming to rest in some edible part.  There are a lot of ways it can get broken down, diverted, or diluted in all of that.  If you want some truly fascinating bedtime reading about the details of animal manure handling, there's at least one good article which summarizes all but the last three links of that chain.⁶  In short, though results vary widely by the type of antibiotic, a significant amount of drug can make it into animal manure, but washing it into storage ponds or pens and letting it sit there until it's used seems to degrade a lot of residual antibiotics.  From there, if it's put on top of the soil, sun can do a real number on some antibiotics, breaking them down fast.  Plus, some of them are really water-soluble and get washed out of the root zone pretty quickly.

Some amount often persists.  What that amount is depends hugely on the steps up to that point, and what type of soil is involved.  If they're present, and studies have documented fields where they are^7,8, some antibiotics have been shown to make it into plant roots⁹, or even whole plants¹⁰... but only in the lab, and sometimes with setups as artificial as soybean plants with the green part lopped off. If they do make it into circulation, the plant may break them down. Plant enzymes have been found which resemble the same ones we have to degrade toxins and drugs, leading to what's called the "green liver" effect.¹¹ Finally, the plant might store antibiotics in some part that we don't eat; if we eat its seeds, storage might be in the leaves.

So when it comes to whether our food plants take up small oily molecules, many of which are also easily assimilated by animals (our cell membranes aren't that different), the answer is... we don't know.  We know it's possible in theory, but we haven't yet determined whether it happens in real life, or whether it affects us.

Could we do testing of plant-based food to determine antibiotic levels?  Sure.  But without also collecting data on all the factors up to that point -- remember all the steps between the feed bag and your table? -- it would be of limited use.  Was the soil sandy or clay?  Was the manure stored before use, and if so, how long?  What was the starting concentration of antibiotic in the manure?  Until we know all the factors, we don't know enough to figure out what to do to reduce the problem.  If it is one.  Maybe it's only an issue in clay soils above pH 6, where pig manure was injected into the soil less than five weeks before planting.

This is a classic case of the frustration built into science.  It feels like a basic question, but the answer is incomplete and unsatisfying... perhaps now you can see that it's just because the question is so big.  To really answer it, we'd have to go through and test each animal antibiotic under all the common situations, for a large sample of the plants we eat.  It's equivalent to taking students from a dozen elementary schools all around the country, and forty years later, trying to find out whether they play golf.  You could make guesses, based on generalities; those from whiter, wealthier neighborhoods are more likely to play golf.  You could ask a bunch of random people, and use those results to estimate what percentage of those people would play golf.  But until you track each one down and ask them, you don't know for sure.  Repeat that process for each crop plant, with each antibiotic, and it becomes a huge task.

If there's anything to take away from this, it's that some of the research on antibiotics and other contaminants is being done.  Enough people feel that it's an issue worth exploring that they have done studies, and those studies have been wrapped into review articles, and those reviews have prompted people to ask more questions.  Hopefully you now have a better idea of what questions are worth asking, and what might make a good answer.

Meanwhile, you can put away the sugar container when planting your tomatoes. :)

What kinds of pollen cause hay fever?

Hay fever is a malady we generally don't associate with winter.  Even in Northern California, the rainy season damps it down for a while (just in time to catch respiratory viruses instead).  Still, depending on what you're allergic to, hay fever can strike almost year-round in warmer climes.  If the humidity is down and the temperature is mild, get ready to buy allergy medication.

Assorted pollen grains (public domain, from
Dartmouth Electron Microscope Facility)

Allergic responses in the airways are caused by all sorts of microscopic particles: dust, mold spores, animal dander, and pollen are major players.  When it comes to pollen, you often hear people blaming various plants -- goldenrod, daisies, sunflowers, wisteria, and even roses have been named by sufferers.  They don't usually include the most likely culprits, such as oaks, evergreens, and grasses.

The major deciding factor in whether a plant triggers hay fever is how it's pollinated.  Plants tailor their pollen, like their flowers, to their pollinator of choice.  For a large class of plants, the main pollinator is simply the wind; they're called anemophiles (anemo means "wind", phile means "loving").  The rest rely on animals of some kind, self-pollinate, or clone themselves some other way.  Insect-pollinated plants are referred to as entomophiles (you might recognize entomo from "entomology", the study of insects).

In order for pollen to cause respiratory allergies, it has to be airborne.  For anemophiles, that's the whole idea: make light, powdery, often small pollen that is picked up and carried easily by the wind.  Some conifers go so far as to put "wings" on their pollen grains.  Flowers are small and quite simple, as their task is largely to get as much exposure to air currents as possible.  Male flowers throw lots of pollen out in the hope that a grain or two will fall on a receptive female flower, somewhere.  (Fun fact: airborne pollen is quite effective at encouraging cloud formation.)¹

Entomophiles, on the other hand, have insects to handle distribution for them.  They make less pollen, and it's more nutritious (to encourage foragers); that added protein and fat content makes the grains heavier.  They're covered with a sticky substance called pollenkitt², which is barely present on pollen made to be windborne.³ The size of the grains doesn't seem to have much to do with the type of pollinator⁴ (in fact the smallest pollen commonly listed is from forget-me-not, an insect-pollinated plant)⁵, but the heavy, sticky nature of insect-borne pollen makes it much less likely to be wafted up into the air.  These plants also make showier flowers, with bigger structures to serve as billboards for their pollinators.  Those structures are what we typically think of as flowers, with color, petals in various arrangements, and sometimes insect-luring scents and nectar.  Sweet-smelling flowers are insect- or bird-pollinated, so unless you stick your nose deep in and take a big whiff, the pollen is unlikely to bother you.

That isn't to say animal-pollinated flowers can't cause hay fever at all... when there's enough of a particular entomophile around, airborne pollen can build up to the point that it can sensitize some people.⁶ But it's unusual.

So what should you be leveling your glare at between tissues?  Look for the plants which don't sport showy flowers.  Conifers, like pine, juniper, and spruce.  Olives, oaks, sycamores, mulberries, ginkgoes, all those trees where you never see a "real" flower on them.  Grasses, with their spiky panicles that rise way above all the leaf blades to get a good shot at the wind (that includes food plants like wheat, rice, and corn).  The rattier weeds, like pigweed, ragweed, Russian thistle, and many other roadside nuisances.  Some culprits are widely planted landscape plants, such as xylosma or London plane tree.  Take care with the plants you choose for your own landscape, and try to lean toward those with conspicuous flowers, or strictly female plants.

As a side note, many people believe that buying local honey can help with seasonal allergies -- but if bees don't visit the plants that put out the worst pollen, how could it?  Not all the pollen that bees collect is from the plants they visit; some windblown pollen settles on them and their preferred plants, and gets picked up by the static charge on their body hairs.⁷ So honey that is largely from clover or orange blossoms will still have small amounts of pine, ragweed, or other anemophilous pollen.  As to whether it helps, there's only a little research out there on honey and hay fever, using rather small patient groups, and the results seem to be mixed.^8,9The bottom line: if allergies bother you, and you don't have a problem with honey, it's worth a try.  Worst case, you get a sweet little silver lining to your seasonal sniffles.

What makes Brussels sprouts bitter?

I originally looked this up in the hopes of giving people advice on how to make their Thanksgiving Brussels sprouts more palatable.  I hadn't really expected what I found.

Brussels sprouts (Creative Commons,
courtesy of Wikipedia/Eric Hunt)

The simple answer is that it's from sulfur compounds common to the broccoli family (Brassicaceae).  The highest-profile of these is sulforaphane, one of several similar chemicals that brassicas use to repel chewing insects and animals, because they taste bad.  (Go figure).  But why are sprouts sometimes bitter and sometimes not, and how can you cook them so they aren't bitter?

Plants respond to stress in various ways.  When they can't get enough water, or the weather is too hot, or they're getting chewed on by bugs or diseases, they produce chemicals to make themselves hardier and less tasty.  Brussels sprouts like lots of water and cool weather, to the point that a few light frosts make them sweeter.  (They build up sugars in the leaves to act as antifreeze when the temperature dips below freezing.) So stressed sprouts are more likely to be bitter, as are ones harvested when they're too mature.  Letting them dry out or sit too long on the produce counter doesn't help either.  If you want the best sprouts, get ones from a major producer or a local farm which are small, rock-hard, and bright green.  The sprouts-on-a-stalk aren't bad either, as they tend to be younger and the stalk keeps them from drying out quickly.  Keep them cold until you're ready to use them.

As for how to cook them, that's more complicated.  Sulforaphone is a potent anti-cancer agent, which goes beyond the usual free-radical scavenging job of antioxidants and actually has the potential to turn on tumor-suppressor genes in cells which are turning cancerous.¹ So really, that bitter taste is good for you, in a much more direct way than just "eating your vegetables".  What's more, it's made by breaking apart a bigger molecule with an enzyme called myrosinase, and that doesn't happen until the plant is injured (such as by chewing).  Myrosinase, like many enzymes, is a pretty fragile protein that is damaged by heating, so the more you cook the sprouts, the less there is.  If you cook them too much, it doesn't matter how much of sulforaphone's parent chemical is in the sprouts, it will never be activated.  (Though you can introduce more myrosinase to cooked Brussels sprouts with the addition of horseradish, mustard, or something like broccoli sprouts.²)

So if you want that anticancer activity, cook them lightly, either by steaming, microwaving on low power, or frying them gently in a pan with a little oil; boiling pulls a bunch of the good compounds out into the water, and heats the enzymes too much. In addition, chewing thoroughly activates myrosinase to make sulforaphone. The catch is that you have to put up with some bitterness, which some people can taste more than others (though we haven't found a clear genetic link yet³). On the other hand, if you have really fresh, young sprouts, they have more than enough sweetness to take off that bitter edge. Kids probably still won't like them, but if you can handle a little hops in your beer or a nice dark chocolate, brussels sprouts shouldn't be any more of a stranger to your diet.

Why do plants in shallow soil end up so short?

This was a real question I fielded last night.  My brother had observed that in areas where the soil is thin -- say, up in the mountains -- the plants there are shorter than their deep-rooted counterparts, sometimes dramatically so.  He said that it seemed to affect all sorts of plants, too, like there was some sort of "as below, so above" rule.  He wasn't sure why.

Photo courtesy of the blogging nurseryman, via Flickr.

He's quite correct; dwarfing is common in plants for various reasons, and one of the places where you really notice it is in areas with shallow topsoil.  Donner Pass in California is a good example: you can look out your car window and see old weathered pines that are only four feet tall.

Just having no room to send roots down doesn't dwarf a plant, though.  In marshy areas, plants can get by with a cupful of soil and send out abundant top growth.  Palms grow tall in lots of places, but their root balls are naturally small (look at pictures of uprooted palms in hurricane areas).  So why the difference?

It's a question of resources.  Plants all need two things: water and nutrients.  In fact, water is the carrier for those nutrients, which get dissolved and taken up into the rest of the plant.  If the soil is shallow, there is no deep reserve of water that the plant can rely on between rains; the soil starts to dry out on the surface, and it's stuck.  As the soil gets drier, it gets harder and harder to pull water out of it, and what the plant can get goes only so far.  Literally: like sucking on a straw stuck into a corked bottle, the plant can get water only so many inches above the ground before it just won't go any further.  Any growth above that wouldn't survive in dry spells.  Some plants can "suck" harder than others, or get by with less water and nutrients overall, which is why some of them end up a bit taller.

Thin soil also tends to be poor in nutrients, as there aren't many things to refresh it (like river silt) and rain easily leaches out what's already there.  Without the basic building blocks like nitrogen and magnesium, plants have to live within their means, and build small.  Add wind whipping around mountain peaks or across deserts, and there are more advantages to hunkering down.  Blowing wind evaporates water from leaves that may be hard to come by, and staying low and dense can help deflect it.

All of this together means that plants which normally grow tall and full, like pine trees, turn into wizened dwarfs where the soil is only a few inches deep.  It's not universal, either among regions or among species, but it's enough of a trend that it's hard not to notice.

Oh, and in case you were wondering, the little pots bonsai trees are kept in aren't what keep the trees short.  Proper bonsai care does involve pruning roots periodically to help them fit in the pot -- but the pruning and repotting leads to a very dense, healthy root system buried in extremely rich soil.  They are kept well-watered, and without diligent pinching up top, most of them would double in size in short order, even with such tiny pots.  Bonsai trees are like miniature athletes in the plant world: fit, vigorous, and pampered.