Author guidelines: what's past is prologue

Last-minute Christmas shoppers are braving the snow and slush outside. I remain sequestered indoors, braving the labyrinthine folds of my own brain. I nurse mug after mug of rooibos, procrastinate by baking these, distract myself by reading that. I find myself at the interface between two parts of my research, you see, and it has taken the form of a mental chasm I am hesitant to traverse.

In reality, I feel most fortunate to have made it this far. New insights into molecular biology are invariably gained using The Scientific Method, and my PhD research has been no exception. The first step is identifying a problem. In my field of study, the problem is that cereal plants manage to protect themselves against the ravages of insect pests, but we don't know how.* The next step is formulating a hypothesis that would address the problem, or some aspect of it. I therefore devised some gene-silencing experiments to test my hypothesis. I spent months in the lab, weeks in the greenhouse and tons of grant money. Most likely, I also inadvertently ate a couple of research subjects (aphids are small). I generated massive amounts of data, crunched the numbers, scrutinized the images, drew the graphs, did the statistics. I spent many hours in helpful discussion with my advisor. And now comes the next step in The Scientific Method: publishing the results.

Ever since I was a child, I knew I wanted to help figure out how the world works. I wanted to add pieces to the puzzle, somehow contribute to our understanding of life itself. Today, I'm fulfilling that dream by investigating the wonderfully complex machinery inside cells that help genes to function. Being a geneticist, with a focus on cereal functional genomics, means the pieces I contribute to the puzzle of nature are rather specific. It all seems rather small. I tend to get caught up in the detail of it. The detail is fascinating, certainly, but sometimes it feels kind of trivial, or unimportant. But then I read Michael Pollan, or about Norman Borlaug and the Green Revolution, or about golden rice, or the looming Ug99 epidemic, and I realize that what I do has tremendous value to world food security. What I do will help feed the world.

That's enough reason to get the word out and publish that paper. It is the final step to The Scientific Method. It also proves one of the most challenging. Which publication does one aim for? Should I be arrogant and aim for a high impact journal, with a very real chance of being rejected? Or do I aim for more a modest periodical and run the risk of my work falling into obscurity? Judging the worth of one's own research is really difficult, especially when you've been intimately involved with it for such a long period of time. The peer-review system ensures that only science of high quality gets published. It also means that the reviewers can be quite brutal, sometimes subjecting your raw data to a full-on audit, of sorts. So I need to be sure before I submit the manuscript. Was the experimental design inherently flawed? Did I include the appropriate controls during gene suppression? Did I transpose a decimal in a calculation somewhere? Are the levels of gene expression truly significantly different between treatments? Alone at night, huddled over my notebooks and spreadsheets, there are moments where I doubt myself. This I have no doubt about, though: with the right kind of angle, this thing will go to press. It deserves to. The story must be told. Without the smallest piece, no puzzle is complete.

And once all of it's over and done with, it's merely chapter one. Further hypotheses and fun in the lab to follow...

*More specifically, we know that so-called resistance genes allow plants to detect the presence of pests such as aphids, and act accordingly. Cereals like wheat can strengthen their cell walls, generate noxious chemicals like hydrogen peroxide - a sort of natural bug spray, if you will - and even kill off their own cells around aphid feeding sites, thereby depriving the bugs of their food supply. What we don't know is how plant defence mechanisms evolved. Nor do we know how they coordinate this massive reprogramming of their biochemistry. Some crop varieties are very good at it, while others do nothing to stop aphids from feeding on them and eventually just wither and die. We don't currently understand why this is the case.

Pimp my petals: the Denver orchid show

There was snow along the highway as we headed for Echter's Garden Center in Arvada. The Denver Orchid Society Fall Show promised to inject some tropical colour into a rather dull October afternoon. The theme was 'Orchids of the World', and I was pleasantly surprised by the diverse amount of species on display. The usual suspects were of course chosen as class winners in their respective alliances: an electric blue Dendrobium victoria-reginae, a denizen of mossy oak forests in the Philippines;


a vibrant Ascocenda Su Fun Beauty, its petals the colour of overripe persimmons;


and Paphiopedilum Magic Lantern 'Memoria Elizabeth Sulzman', holding its pouch as if the plant itself had just blown it from pink bubblegum. Feed me, Seymour, indeed.


Many strange and unusual specimens were on show, to the delight of jaded orchid enthusiasts bored by saucer-sized vandas and over-hybridized cattleyas. This South American Zootrophion below is a prime example of the bizarre orchids on display. Its small cage-like flowers don't open fully, and are covered in tubercules. What sort of minute insect is brave enough to crawl inside these to pollinate them?


Cleisocentron merrillianum is an astonishing little beast from Borneo: its slate grey flowers had many visitors to the show fiddling with the macro settings on their cameras.


Easily overlooked, Eria coronaria had its flowers hidden away in lush green foliage. This fragrant species has a wide distribution and can be found from the Vietnamese coast all the way to the foothills of the Himalayas.


This sinuous monopodial with subtle chartreuse coloured blooms is called Christensonia vietnamica. It originates in Vietnam - as should be obvious from its name - but curiously was unknown to science until as recently as 1993! It was a real treat to see a newly discovered species thriving in cultivation.


As usual my favourite thing on show is a dendrobium - usually a crystalline white Formosae-type with little black hairs on the canes, or a candy coloured jewel from New Guinea. This time Dendrobium bracteosum won me over: masses of waxy flowers emerging from papery bracts on the pendulous canes. This New Guinea native positively froths over with blossoms, each dotted with a rather impudent splash of tangerine on the lip.


Although I've been awfully good since living in the States, this time around I just couldn't help myself. The lure of the sale tables was just too strong, and I bought my first (non-grocery store Phalaenopsis) orchid since moving to Colorado in 2007. I managed to get a totally sweet deal on a Psychopsis Mendenhall 'Hildos' from Oak Hill Gardens. The clone I obtained, 'Hildos, has been awarded a First Class Certificate, the highest award bestowed by the American Orchid Society. So I got a great looking plant from awesome genetic stock for less than the price of a steak dinner. Below is a photograph of a similar orchid that was on show: Psychopsis Mendenhall 'Lace' x Psychopsis Mem. Bill Carter 'Mendenhall'. Are you jealous yet?



I have many more images from the 2009 Denver Fall Show and previous orchid shows available in glorious Technicolor™ on Flickr. Check it out.

Grad school has swallowed me alive

Yes, I'm still alive. And doing rather well, thanks for asking. Unfortunately grad school has become my whole life this past month or so. I have been silencing genes and counting aphids until it feels my head has been drained of grey matter and stuffed with balls of cotton wool. There are several new stories carefully packed in that cotton wool, of course, but you will just have to be patient with me. In the mean time, here are some images from my research, to tide you over until the next proper installment of (E&E)². The top image shows 3,3'-diaminobenzidine staining in a leaf of resistant wheat after feeding by aphids has caused the massive release of peroxides. The bottom aniline blue image is of callose deposits that strengthen cell walls in response to the little suckers.

Sometimes sciences can just be about pretty pictures, can't it?

Ambergris: perhaps you'd rather not know

I combed the beaches of St. Francis Bay with my aunt one afternoon, now a lifetime ago. The weather was nasty; it had been raining for most of the day. We didn't mind, of course, since we knew that stormy weather brings the secrets of the sea ashore. That was the day my aunt found the giant eggcase of a paper nautilus, wedged between the rocks. The perfectly white, rippled object was the most gorgeous and delicate thing I had ever seen. I believe that was the first moment my impressionable young mind was filled with a sense of awe at the mysterious creatures that live in the liquid parts of the planet.

Some things that wash ashore are less obviously beautiful: broken jellyfish, reduced to lumps of snot; kelp fronds; dead gannets; ambergris. Ambergris? Yes, ambergris, the stuff of myth and poetry. Sounds romantic, but what exactly is it? Read on, although the story isn't for the squeamish. Sometimes, when something is so... biological in origin, it is perhaps better to live in ignorance.

The sperm whale is the largest predator to have ever existed. It dives to almost three kilometres below the surface of the ocean in order to do battle with giant and colossal squid in the inky depths. Although sperm whales also feed on fish, they are particularly fond of cuttlefish and squid. The problem with a diet high in cephalopods is that those sharp squid beaks are not exactly digestible. So in a process analogous to how a pearl is formed in an oyster through constant irritation, the whale encases these beaks and other indigestible matter in fatty secretions from its digestive system. These lumps are then easily excreted by the whale, without fear of internal nicks and scrapes.

Many people refer to ambergris as "whale vomit", although Hal Whitehead, a whale scientist of Dalhousie University in Halifax, Nova Scotia, is of the opinion that ambergris is more likely excreted via the faecal route. Not to worry; I won't go into much more detail concerning cetacean scatology. The interesting part of the ambergris story concerns what certain land living bipedal primates elect to do when they find the stuff washed up on the shores of the world. Tar-black and viscous, freshly expelled ambergris is strikingly foul-smelling. However, a counterintuitive thing happens when these lumps drift around in the ocean, exposed to sunlight, oxygen and salt water. As ambergris oxidizes, it begins to cure and harden. Well-aged ambergris has a waxy texture and is marbled grey in colour. In fact, the word ambergris is derived from the French ambre gris, meaning grey amber.

The smell of ambergris fortunately also changes with ageing. People try in vain to describe its depth and complexity, but fail. In the end, ambergris smells like ambergris and there's nothing quite like it. It is sweet, but dangerous. It has earthy notes, like tobacco, mulch or mossy pine forests combined with marine notes like sea spray and ocean breezes. But it also exudes something that belies its animal origin: musk, leather and something altogether mammalian. Like the flowers of jasmine, it retains a definite faecal undertone. The elaborate chemistry of ambergris consists of countless compounds, and is particularly abundant in steroid lipids. The most important of these is a molecule called ambrein, pictured here. Ambrein is oxidized during the ageing process, to form several related pungent compounds with names that make them sound rather like the heroines of forgotten Victorian bodice-rippers: ambrox, ambroxide, coronal, ambrinol... It's the combination of all these molecules together which is responsible for the complex fragrance of ambergris.

Gross as its origins are, ambergris has been a highly valued commodity for centuries. Reknowned in China before the year 1000, it was known as lung sien hiang, meaning "dragon’s spittle fragrance," because it was thought to be the saliva of sleeping sea dragons drooling into the ocean. During the Renaissance, small lumps of ambergris were moulded into decorative jewelry. It was ceremonially burned, like incense. It has since found particular use in the perfume industry as a fixative. It retains other fragrance ingredients, preventing their rapid evaporation and allowing the scent to linger on the skin. One classic method for preparing an ambergris extract used "1½ oz. of ambergris, 30 grains musk and 20 grains civet reduced to powder in loaf sugar," to which was added the juice of 1 unripe lime. This was poured into 3 pints of pure spirit alcohol and placed in a stoppered jar. The jar was incubated in "the constant heat of horse manure for 21 days," and the resultant clear, amber-coloured liquid decanted as Tincture of Ambergris. Perfumiers today rely on more scientific methods of extraction, or have switched to using synthetic alternatives. However, real ambergris is purportedly still an important component of such famous fragrances as Chanel No. 5 and Drakkar Noir.

The quality of ambergris depends on how long it has been floating around the ocean. Just like wine it mellows with age, and increases in value. Standard grade ambergris trades at almost $20 per gram. Considering that ambergris is sometimes found as giant lumps weighing hundreds of kilograms, finding ambergris on the beach can be quite lucrative. Since ambergris resembles a smelly, shapeless lump of sea detritus and not the delicate eggcase of a paper nautilus, most people ignore it witout realizing its value. Pieces of the fragrant flotsam are often sold for tens to hundreds of thousands of dollars to so-called "ambergris brokers". The trade in ambergris seems slightly shady: deals occur behind closed doors in hotel rooms in places like Dubai and Abu Dhabi, and purchases are always made in cash. Just a few people control the world ambergris market, and I suppose they would like it to remain that way.

Through the ages, ambergris has not solely been used for perfume. Its animalistic allure had much further reach. In fact, it formed a vital part of the traditional pharmacopeia of many cultures around the world. It was lauded as a restorative balm. Arab doctors prescribed it as heart and brain medicine. Perhaps not surprisingly, the sensual scent of ambergris was highly in demand as an aphrodisiac. Legend has it that Madame du Barry washed herself with it to make herself irresistible to Louis XV of France. Oddly enough, ambergris has been - and in some cultures still is - used as a spice for food and wine. Beluga caviar? White truffles? How gauche. Surely shavings of first grade ambergris on your eggs benedict must be an unparalleled epicurean billionaire's treat! Personally, I'm sure I could never stomach it. If it disagreed with the whale, it is certain to disagree with me.

Picture credits: paper nautilus © mrpbps; sperm whale © Brian J. Skerry; ambergris © composite from various sources; Chanel No. 5 © Andy Warhol, 1985; vintage perfume bottles © meeralee.