GMO methods

Here's where we get into the real nitty-gritty science of genetically modified organisms (GMOs): the technology used to make them.  I defined (mostly) what a GMO is in the last post; now we see just what the methods are which set them apart.

A. tumifaciens Ti plasmid, courtesy of BacMap

Gene splicing of this sort really took off some thirty years ago, when the first trials of herbicide-resistant tobacco were done in the U.S. and France.¹  Many lab experiments had been done over the previous decade, but when the tobacco field trials were done, along with the test of a spliced bacterial strain that successfully helped protect a field from frost damage,² the era of commercially viable GMOs had arrived.

Since then, the specific technologies have changed a bit, but the process remains the same. I'll lay it out, step by step.

Step 1: Identify the gene you want.

This could be a gene from a mutant of the same plant variety, a different variety, a different but related plant, a wildly different plant, or something from another kingdom entirely, such as bacteria or animals.  The more closely related it is, the easier it is to get the target plant to express that gene (read it and make a functional protein).  But there are a few tricks to get even foreign genes to work.

Gene sequencing has made selection a lot easier.  We can compare the genetics of the plant we have with those of a plant that does what we want, and pinpoint genes which might be responsible for the difference.  We have maps for what all the genes in some simple organisms do, such as some bacteria, and we can use those to find genes that look similar in other things.  And there are methods to "knock out" the genes we're interested in, to see whether the feature goes away.

So once the researchers have picked out what looks like a good candidate, the next thing is...

Step 2: Isolate the gene.

There are a bunch of little steps here, all with the same goal: get a specific tidbit of DNA into the open.  First all the DNA is pulled out of the cells in a sample, and washed clean of the remnants of cell wall, cellular machinery, and so on.  Then an enzyme or two is added to the DNA, to break it into bite-size pieces; the enzymes used have particular sequences they like to "snip" at, and one is picked which will cut as close as possible to the target gene, but leave it intact.

Since there still isn't a lot of material to work with, the bits are run through a process called polymerase chain reaction (PCR), which multiplies the target gene over and over.  Ideally, with good primers (the "hooks" used to fasten on to the piece so it can be multiplied) only that gene is amplified, and it comes out with thousands or tens of thousands of copies.  Then it's separated out from anything else in the solution, and you have your little vial of the copied gene.

Step 3: Add some extras.

Most of the time, a new gene won't get used in the plant it's put into.  Or, if it is, it won't make as much as we want of the protein it codes for.  How often a gene is used is controlled, largely, by promoters: little sequences at the beginning of the gene which tells the cell when to use it.  A plant virus known as Cauliflower mosaic virus (CaMV) came up with a couple of promoters of its own, which it added to the genes it inserted into its host during infection.  The main CaMV promoter, known as 35S, is "always on"; if the promoter is there, the gene it's attached to gets expressed all the time, and cranks out lots of orders (RNA transcripts) for its protein.³  There are other promoters used in making GMOs, including another from CaMV, but the 35S promoter is still very widely used.⁴

Once you've got your new plant, how can you tell whether your gene actually got into it?  Many insertion methods are pretty chancy.  Therefore, having some easy way to tell your gene is in there is helpful.  As a result, there are a bunch of available marker genes,⁵ which give the new plant some new, harmless ability which it's easy to test for.  They include selectable markers, such as antibiotic resistance (kanamycin is common), and reporter genes, which make some substance which can be seen or tested for chemically.  The gene for green fluorescent protein (GFP) makes a protein that glows under blacklight, and GUS creates a stain when an enzyme is used on a test cell.

These markers are typically tacked onto the desired gene before packing the whole thing up, and they are present in the mature modified plant.  That said, they're pretty useless in the field, and unlikely to have any effect on the plant's survival or the animals who eat it.  There's been more of a question about the effect of the promoters, but I'll go into that in a later segment.

Finally, we're ready to...

Step 4: Get the gene into the plant.

There are a bunch of ways to do this.⁶  The earliest method for introducing genes into plants used a bacteria called Agrobacterium tumefaciens, better known as the cause of crown gall (if you grow roses, you might have heard of it).  A.t. has a loop of genetic material which can cut into the DNA of just about any non-grassy plant, and insert its cargo of a handful of genes.  Scientists took that carrier loop, known as a plasmid, and deleted the native A.t. genes; then they could splice in anything they wanted.  All they had to do then was to breed up a bunch of these bacteria, with their new genetic cargo, and let them infect some cells from the target plant.  It worked pretty well, as methods go, and it was the means used to create the first generation of genetically modified plants.

Beyond Agrobacterium, there are some viruses that can also carry genes when they infect a plant, and viruses or other bacteria which can modify bacterial GMOs.

When a plant cell is stripped of its cell wall, so that all it has is a cell membrane similar to those of our own cells, a small electric shock can open up holes in the membrane long enough to slip some DNA in.  If it's done right, that DNA is taken into the cell and treated as if it belonged.  Specific chemicals can have the same effect of temporarily punching little holes in the cell membrane to allow new genes in.  These methods, electroporation and chemical poration, are much more successful than Agrobacterium at modifying grassy plants.  Vacuum infiltration, using vacuum to open up cell walls enough to infuse genetic material, has a similar end result.

Microinjection uses a small needle to inject DNA into plant cells.

Finally, the most recent and most widely applied category of modification is bioballistics.  The DNA cargo is loaded onto tiny "bullets" made of tungsten or gold, which are then fired at the plant like a shotgun.  Some of those bullets penetrate cells and drop their cargo, which is then taken up.  It sounds very haphazard and inefficient, but it works surprisingly well, and has been used to create many of the newer GMOs.  It helps that this "gene gun" works on grassy plants, such as rice and corn, which can be hard to modify by other means.

Step 5: Make a new plant.

Now that you've got the gene into the plant... but wait, it's only in a handful of cells at this point.  The next thing is to make whole plants, where every cell is modified.

In some cases, like bioballistics, the embryo of a seed can be the part modified, so it's pretty simple to grow it up into a whole plant.  With Agrobacterium modification, chemical poration, or electroporation, it takes some work, because the cells that have been modified are random tissue cells.  Fortunately, plants have the ability to grow whole new individuals from any single cell, if the conditions are right.  The procedure to do that is called micropropagation, or tissue culture, and it's used for other purposes such as creating disease-free plants from virus-infested parents.⁷  With time and care, the individual modified cells are coaxed into making roots and shoots, and finally they're indistinguishable from those grown from seed.  It's more difficult with grassy plants, though many of the problems have been solved over the years.

At this point, the plants can be test-grown in the greenhouse to make sure they grow properly and have all the desired traits.  In many cases with crop plants, the last step is...

Step 6: Breed a new variety.

Plants which are easy to modify aren't always the ones that offer the best performance as a crop.  So, once it's clear that the target gene (the transgene) has successfully made it into new plants, those modified plants are bred with a high-yielding commercial variety, using traditional methods.  The offspring are examined to make sure they still have the transgene, and several generations down the road, the new variety is stable and ready for general use.


So there you have it.  The process of creating modified plants has brought up a bunch of questions (separate from those raised by the genes themselves), including some about the safety of the promoters, how genetically stable the new plants are, and whether randomly-inserted genes might disrupt the plant in such a way that it would become harmful to eat.  I'll address those issues all together in a later segment, under "Concerns".

Next up: which plants, and which genes, have been thrown into the GMO pool so far.

[This article is part of the series on GMOs. Jump to the first post for an overview and index.]

GMOs defined

When talking about genetically modified organisms (GMOs), it helps to start by defining them.  To that end, let's see what definitions the various authorities use.

Steffen Dietzel, courtesy of Wikimedia Commons

The Random House dictionary definition:
[A]n organism or microorganism whose genetic material has been altered by means of genetic engineering.

Merriam Webster doesn't have a definition of GMO, but defines genetic engineering:
[T]he group of applied techniques of genetics and biotechnology used to cut up and join together genetic material and especially DNA from one or more species of organism and to introduce the result into an organism in order to change one or more of its characteristics.  (Take a deep breath after that one.)

The World Health Organization's contribution:
Genetically modified organisms (GMOs) can be defined as organisms in which the genetic material (DNA) has been altered in a way that does not occur naturally. The technology is often called "modern biotechnology" or "gene technology", sometimes also "recombinant DNA technology" or "genetic engineering". It allows selected individual genes to be transferred from one organism into another, also between non-related species.

The European Union's legal definition:
An organism is "genetically modified", if its genetic material has been changed in a way that does not occur under natural conditions through cross-breeding or natural recombination.¹

Finally, the US Food and Drug Administration's regulatory definition:
In the case of foods, genetically engineered plant foods are produced from crops whose genetic makeup has been altered through a process called recombinant DNA, or gene splicing, to give the plant desired traits. Genetically engineered foods are also known as biotech, bioengineered, and genetically modified, although "genetically modified" can also refer to foods from plants altered through methods such as conventional breeding.

So there you go -- clear as mud.  However, the general consensus is that genetically modified organisms are plants (or animals) altered by individual-gene splicing methods which have been developed in the last 30 years.  The term "GMO" generally refers to organisms deliberately modified by viruses, bacteria, "gene gun", injection, electrical shock, or chemical poration, to carry a specific set of new genes that they didn't have before.  It doesn't usually include mutation (by radiation or chemicals), so-called "wide crosses" where distant cousins are bred together, various hybrids, or cloning plants from a single cell or growing point.

Even before the advent of real gene splicing, we were messing with our food to a serious degree.  Many people point to corn, which was bred up from a grassy weed, as an example of how we've always manipulated food plants.²  What I think of, however, are the more recent developments of ruby red grapefruit and seedless watermelons.  "Star Ruby", the first of the seedless red grapefruits, was the result of treating grapefruit seeds with radiation.³  Seedless watermelon plants are hybrids, made by crossing a regular watermelon with one which has been treated with a chemical to double its chromosomes; the child of that cross has three of each chromosome, which short-circuits its seed production.⁴  It would have taken hundreds or thousands of years to breed these plants by traditional methods, though it is theoretically possible.  Both mutations and doubled chromosomes happen in nature.

GMOs, by contrast, couldn't be made using old-world methods at all.  One of the definitions of species is whether two individuals can successfully breed; a plant (corn) and a bacterium (Bacillus thuringiensis) are too far apart to cross.  We have enough trouble breeding together cousins like wheat and rye, and only succeeded with the aid of the chemical colchicine.⁵  So a crop like Bt corn, which has genes from Bacillus thuringiensis inserted into it to repel pests, could only come out of the modern methods I mentioned above.

Now that we have some idea of the result, the next step is to look at those methods.  That will be the next post.

[This article is part of the series on GMOs.  Jump to the first post for an overview and index.]

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.