I love thial-S-oxides so much I cry

Lots of things can make us cry. Pain. Joy. Boredom. Sadness. Toy Story 3.

There’s another common source of tears in any home, and it lives in the kitchen. Onions and other plants in the Allium genus produce compounds that trigger an involuntary reaction. Chopping these bulbs turns even the most stoic into a weeping mess in minutes.

What makes this happen? Does the onion want us to be sad? Does it want us to share in its misery? Does it want to inflict the same pain upon us that we inflict on it? How does a simple vegetable have that much power over our tear ducts?

The answer lies in biochemistry. Despite their unassuming appearance, onions pack powerful chemical weapons, ready to launch upon us at a moment’s notice. The main compound produced by onions is called the lachrymatory factor. This chemical has an unusual chemistry for a biological molecule, because of one atom. Sulfur.

It's just **sniff** so beautiful!
Lachrymatory Factor

If there’s ever weird chemistry happening in the cell, you can bet that sulfur is probably involved. Let’s explore why.

Smelly yet invaluable: the versatile chemistry of sulfur

Sulfur is interesting in biological chemistry because it can do much more than most other abundant biological elements. In its simplest form, sulfur can link up with hydrogen, to form H2S, the main ingredient of sewer gas and other unpleasant biological emissions. If you ever run in to a smell like rotten eggs, there’s a good chance sulfur is involved.

Sulfur’s superpower is its large number of stable oxidation states. A common and stable form of sulfur is sulfate, when the sulfur is linked to four oxygen atoms. Three oxygens is a sulfite, two a sulfinic acid, and one gives you a sulfenic acid. This versatility lets molecules with sulfur do a lot of things that other biological molecules can’t.

Sulfur can also form more complicated compounds when you add in carbon and nitrogen,  creating compounds like vitamins B1 (thiamine) and B7 (biotin), antibiotics penicillin and  sulfanilamide, and the critical biological molecule coenzyme A.  Sulfur also forms an integral part of protein molecules linking to carbon atoms in the amino acids cysteine and methionine. The sulfur atoms in cysteine can link with itself to form disulfides, an important part of its role in protein molecules. It can also link to oxygen atoms in a variety of ways, which let it respond to the oxidative environment, build unique compounds, including many with biological roles.

Because sulfur is happy to ignore the common rules of molecular bonding that carbon, nitrogen, and oxygen tend to obey, if frequently is used when non-typical chemistry is needed. Cells use a sulfur-containing cofactor to shuttle methyl groups around the cell, and use the sulfur-containing vitamin B1 to carry out many complex biochemical transformations.

Lachrymatory factor is another great example of this chemical versatility. The compound is an S-oxide or sulfoxizime compound. This means it carries a positively charged sulfur and negatively charged oxygen atom, directly bonded to each other. This breaks a rule that we teach in organic chemistry that you cant form stable covalent molecules with positive and negative charges adjacent to each other. Unfortunately, this is one of those rules that is more of a guideline than an actual rule, and sulfur is happy to ignore it.

pirate barbossa

That said, this arrangement of atoms in the lachrymatory factor is not stable over the long term, so it can’t be made in advance and stored for long amounts of time. It’s also a gas, so hard to contain within a plant’s tissues. So how does the onion release it so quickly when you cut into a bulb?

It’s got a hell of a defense mechanism. You don’t dare kill it!

In the Alien series, the blood of the xenomorph creatures is toxic and corrosive. Attack and injure the alien, and it spews this toxic acid, corroding whatever it comes into contact with, including any humans foolish enough to attack in the first place. This serves as a pre-emptive defence for the alien. Hurt me, you’ll get hurt, too.


The same strategy plays out with many plants. Plants can’t move in response to predators, so they protect themselves in a different way, with chemistry. When their cells are damaged, they produce noxious chemicals to turn away their predators. These chemicals can take many forms and actions, sometimes poisoning us, often having no effect, but sometimes having beneficial pharmaceutical properties, that help us treat disease. In fact, many potent pharmaceuticals come from plants.

Lachrymatory factor plays this role for onions, in the same manner as allicin does in garlic, and a different class of sulfur-containing compounds does in cruciferous vegetables like broccoli. Herbivores or insects who try to eat the plant will be overwhelmed by noxious chemicals, and look elsewhere for their dinner. But how does the onion actually make the compound when it’s injured?

Red Light, Green Light

Onions generate the lachrymatory factor on the spot, immediately after tissue damage. It does this using a smart solution – keep the two elements that generate the noxious chemical separate, and only allow them to come into contact if tissues are damaged. Onions generate the lachrymatory factor by breaking down precursor molecules using enzymes called alliinases. This releases the lachrymatory factor into the air, to wreak havoc on our tear ducts.


Onions keep these precursor molecules (alkyl cysteine S-oxides) and the enzymes needed to make them in different compartments, so they do not normally meet. When you slice into them with a knife, the cells are broken and the enzyme and precursor molecules meet. As the enzyme starts to break down the precursor, it releases lachrymatory factor*, which diffuses into the air. This reaction happens fast, but not instantaneously, which explains how it can take a minute or two for the vapours to accumulate enough to cause problems. As soon as the plant is damaged, it starts producing lachrymatory factor, but it takes a few minutes to accumulate enough to affect us.

Protecting yourself from lachrymatory factor

If you feel you’re a tough individual, it can be pretty embarrassing to break down in tears in the kitchen. That should be reserved for when you finish reading Where the Red Fern Grows. So how can you keep the onion tears away?

Chemistry to the rescue

We know two things: First, lachrymatory factor is produced by onions in response to injury when enzyme and precursors come together. Second, lachrymatory factor is a gas that is released from the onion’s tissues into the air around us. Based on these two facts and the basic principles of chemistry, what can you do?

  1. Work fast. It takes time for the alliinase reaction to take place, so the shorter the time freshly cut onion is in the open, the better.
  2. Use ventilation. A fan (preferably one that vents outside) can whisk the vapours away.
  3. Cool everything down. Enzymes work much faster at room temperature than at refrigerator temperature, so cold onions will produce less compound. Gases are also less volatile at colder temperatures, which also reduces how quickly it migrates into the air.
  4. Once it’s cut, heat it all up. Once an enzyme is denatured, it’s dead and doesn’t work any more. Enzymes can be denatured by cooking, and sometimes by acidic or basic treatment. Another reason to work efficiently – get those onions cooking, and they’ll stop making the chemical pretty quickly.
  5. Onion Goggles? No. Don’t do this. Just don’t.

A tear-free onion?

So, if we know just how this noxious chemical is produced, is there any way we could reduce it altogether? This has been done by a group in 2008. By reducing the amount of one of the enzymes involved in making lachrymatory factor, researchers could greatly reduce the production of the chemical from these onions. In the process, the onions even seemed to make more of other flavourful, sulfur-containing compounds, so this work certainly looks promising. One interesting consideration with a lachrymatory factor-free onion is that it might be a lot harder to grow – the chemical is a form of defence against herbivores and insects, after all!

Not much word on this work since then, but if it isn’t already underway, I’m certain new technologies might make this even more feasible in the near future. Every time I make dinner with onions, I’m reminded and hope we get one soon. A tear-free onion can’t come soon enough for me.

*Technically, it releases an intermediate that is then converted by another enzyme to the active lachrymatory factor, but for the sake of simplcity we can pretend the compound is produced immediately

Eady CC, Kamoi T, Kato M, Porter NG, Davis S, Shaw M, Kamoi A, & Imai S (2008). Silencing onion lachrymatory factor synthase causes a significant change in the sulfur secondary metabolite profile. Plant physiology, 147 (4), 2096-106 PMID: 18583530

Poor Public Understanding is Killing Basic Research in Canada

This post is cross-posted from a blog post I wrote for the Science and Policy Exchange on December 1. For more insightful writing on science and how it relates to government, the media, and society at large, visit their site http://www.sp-exchange.ca

Years ago, I worked for the summer on my neighbours’ cash crop farm. We mostly worked with cabbages. It smelled terrible. My coworkers, tough guys in their forties, learned I was studying in the sciences, and had no end of recommendations of useful things I could do with my degree.

“Hey science-boy! You should make some cabbages that bugs won’t eat!”
“Hey science-boy! You should make cabbages that keep better in storage!”
“Hey science-boy! You should make stackable square cabbages!”

picOf course these comments weren’t serious, and came from small everyday frustrations on the job, but the assumptions behind them are interesting. These men viewed science solely as a tool to produce innovations, and by extension, to make their lives easier. I don’t think their attitude is unique. For the most part, today’s lay public views science as something that makes new smartphones and performance fabrics, not much more.

This is a problem. Science doesn’t work well when it’s focused at specific applications. When you work in the realm of uncertainty, one of the only things you can have confidence in is a high rate of failure. Spreading initiatives broadly and pursuing the most interesting questions as they arise is a more efficient use of resources, and improves the chance of success. This is especially important when we remember that many (most?) great innovations come from serendipity, not planned investigation, so the wider we spread our inquiry, the more likely we will hit upon something that will drive technology forward.

While fundamental science is poor at developing specific solutions, it excels in discovering new principles. Sometimes these principles can translate directly into commercial products, but more often they form part of an accumulated wisdom that moves our understanding incrementally forward. The useful applications emerge naturally, albeit slowly, from that understanding. But that’s boring. And certainly isn’t a compelling story.

What is a compelling story?

Innovative new technology will convert industrial greenhouse gas emissions into commercial products

Canadian companies developing natural health products will be able to get science-proven, competitive new products on shelves faster

“Canadian firms will now be able to transform agricultural and forestry by-products to create new materials and reduce the use of petroleum-based polymers (plastics).”

The amount of certainty in those statements should make any scientist bristle. It betrays a misunderstanding of the scientific process and a fundamental arrogance that the result is predetermined, not subject to any uncertainty. These projects are part of the National Research Council’s new mission to shift “the primary focus of … work at NRC from the traditional emphasis of basic research and discovery science in favour of a more targeted approach to research and development”.

At the NRC and other government research institutes across Canada, the research climate is moving towards projects with the potential to produce marketable products, away from pursuit of understanding of the world around us. Government-funded research agencies across the country are being retooled to stop looking outward and pursuing novel ideas, instead turning inward, transforming into glorified factories. This is an extremely short-sighted strategy, crippling our capacity for innovation.

If I’m generous, the politicians enacting these changes are influential laypeople, at least as far as science is concerned. They don’t recognize that the long-term benefits of fundamental research are being lost as they focus myopically on risky but sexy-sounding megaprojects. If I’m a little more cynical, they realize that the public thinks science exists solely to produce new products. They exploit this by claiming they’re working to improve the lives of the average Canadian, and will include that in their re-election platform. The amount of times the term “strengthening our economy” gets dropped into government research press releases suggests the more cynical interpretation.

So what needs to change? To start, those in power need to recognize the importance of fundamental research to the long-term health of a society. We’re on a treadmill moving forward, and if we don’t keep pursuing challenging questions, we fall behind. More importantly, the public perception of science has to change. As long as Mike from Canmore is happy that his tax dollars are propping up companies instead of pursuing important fundamental discoveries, nothing will change. Scientists need to hold politicians accountable, but more importantly, they need to educate the public on the importance of pure research to long-term innovation. The layperson needs to know that pure research is a long-term investment that pays economic dividends many election cycles into the future.

The current direction of government-funded research in this country is troubling. Without public understanding of the importance of fundamental research, the trend will continue, and the foundations of our research apparatus will continue to erode. However, there may be one positive effect – my coworkers might finally get those square cabbages.

Edit 2015.09.02: I’ve updated my account since I first wrote this post. If you’d like to follow me online, find me @superhelical