Tuesday, 28 June 2011

I've Got a Lovely Bunch of Coconut (Genetics)

If the venerable gentlemen of Monty Python have taught me anything, it’s that there is a lot you can do with coconuts. While making horse-clomping sounds and ad-hock bikinis spring to mind, researchers are using these psuedo-nuts for a more academic pursuit: studying early human movements in the southern seas. More than just delicious tropical beverage containers, coconuts can tell us a lot about travel and colonialism thousands of years ago. From DNA to ancient trade routes, scientists are shining a light on ancient history with modern biology.

photo credit: www.hotbeautyhealth.com
We might worry about long weekend traffic when setting out for a summer getaway, but we rarely stay home for fear of inadequate food and drinking water. A concept that is often overlooked in our grocery store culture is how much the availability of food has shaped our societies. Case in point: human exploration and societal expansion in the tropics was directly influenced by the coconut. Not only did this fruit-bearing palm provide a convenient source for a key piƱa colada ingredient, it also represented a portable source of water, oil, fuel, and building materials. By virtue of these life-sustaining qualities, this single plant played an enormous role in the ability of would-be navigators in the southern Pacific and Indian oceans to exercise their sea legs thousands of years ago.

            As Sir Isaac Newton so eloquently phrased his own musings on coconuts: “every action has an equal and opposite reaction.” While coconuts were enabling early globetrotters to set sail, these same expeditions were helping to spread the coconut plant throughout the tropics. Furthermore, people were cultivating coconuts to have specific human-friendly traits. Shorter, self-pollinating plants bearing rounder, juicier fruit allowed people to spend less time climbing and growing palm trees, and more time chowing down on sweet coconuts. From this point of view, our societies are built on what we eat, but we also have a formative influence on our dinner. Ah the tangled food webs we weave.

            Now that we know just how tied up our early exploratory urges were with coconuts, how can these fibrous historians give us insight on human history? The answer lies, like so many things in this genomic age, in their DNA. Researchers compared genetic markers from 1322 coconuts from all over the world and used this information to trace the development of modern coconuts from various geographic locations. They found that coconut cultivation was started independently in two locations: the outskirts of the southern Indian coast, and the south Asian seas between the Malay Peninsula and New Guinea. What's more, they could trace ancient nautical trade routes connecting Madagascar and southeast Asia by observing where the genetic signatures of the two lineages mixed. Coconuts growing on these ancient trade routes still have blended genetics, while those growing in environmentally similar conditions but off the main drag clearly belong to one group or the other. This data, and associated historical records, also shows the Philippine origin of Panama coconuts planted 2250 years ago, that the Spanish brought coconuts from the Pacific to Mexico, and how Caribbean coconuts brought by Europeans were originally picked up in India.

The ever-present human urge to modify and exploit our surroundings usually results in a fascinating tangle of anthropology and biology. No man (or society) is an island, but without each other, both us and the coconuts might have been stuck there.

Wednesday, 22 June 2011

The Best Laid Plans are Bound to Grow your Rye

Photo Credit inhabitat.com
There are three certainties in life: death, taxes, and the amazing ability of natural selection to produce surprising results. From clownfish making a home in the tentacles of venomous anemones to the poop-eating fly, every niche gets filled and every resource gets used. But what happens when us notoriously destructive humans come into the picture? It turns out we’re not only destroying habitats by building houses, we’re also creating new ones in some pretty surprising places. Who knew your dishwasher could be so cozy?

            Before we venture into what’s colonizing our kitchens, let’s explore the idea of ecological niches and how they drive evolution. In simple terms, and ecological niche is any living thing’s role in its community. The waitress in your community serves you lunch, but also occupies a home, takes the bus to work, and buys bread from the bakery. Her niche in the community is not only what she does, but how she contributes to what everyone else does and where and when she moves around. Everyone has a niche: doctors, homeless people, cashiers, teachers, raccoons, moths, viruses, and fungi.

            Everything in nature occupies a specific ecological niche. If too many organisms have the same role (fill the same niche) in a community, the competition for resources makes it hard for them to make ends meet. Picture a neighbourhood with too many piano teachers: there are just not enough students (and paying parents) to go around. If one of them starts teaching children’s art classes, however, they can collect cash from a whole new set of parents. By using the community resources (ie. bored school kids) in a new way, the various teachers are able to coexist. This is essentially what happens in nature and is one of the major forces driving evolution.

            The pressure to use all available resources results in species that live in some pretty extreme environments. Think of the tubeworms in the boiling ecosystem around hydrothermal vents, fish in acidic caves, and black yeast growing in your dishwasher. That’s right, ecological niches can be man-made too, and some can be just as extreme as those found in nature. The dishwasher, for example provides an environment with intermittent hot temperatures, tons of moisture, and high pH (due to the dish soap). What it also provides is lots of food; after all, that’s what we’re trying to clean off the dishes in the first place. This valuable resource is not accessible to many organisms, but the few that can tolerate the harsh conditions can set up shop and thrive in this newly created household niche.

            Lots of spaces in our towns, cities, and especially bathrooms are great new habitats for the homemaking. Unfortunately for us, some of our microscopic roomies can prove pretty temperamental. Antibiotic-resistant bacteria in hospitals are the result of an environment with lots of these chemicals. Heat-tolerant and potentially harmful black yeast are evolving to fit a very family-adjacent niche thanks to our hatred of hand-washing dishes.

            You can’t control everything, humans. The very areas we create as unlivable will always be taken advantage of by something that thrives in just those conditions. Every once in a while we have to take pause and remember: evolution is one bad grabba-jabba!

Tuesday, 14 June 2011

The Real "Scrubbing Bubbles" are Green and Slimy

If you asked most people about their favourite use for algae they might have some trouble coming up with a reply. Although my own preference is to have it wrapped around a tasty California roll, those who don’t share my obsession for this oriental treat might be interested in algae as a versatile ecological engineering tool. In true “But wait, there’s more!” fashion, algal turf scrubber technology is making progress in water quality improvement, reduction of commercial fertilizers, and biofuel production.

            Before delving into its potential for mopping up our planetary mess, what exactly is algae? “Simply” put, algae are “simple” plants. Plants because they are able to make their own food (autotrophic) through photosynthesis, and simple because their tissues are not differentiated in the same way that land plants are. Flowers and trees have tubular structures (vasculature) for nutrient transport and structural support. This includes root systems, leaf veins, and tube structures in trunks or stems. Aquatic algae don’t have this vascular system as their soggy environment creates natural buoyancy and helps move nutrients within the plant. Algae come in many varieties, all the way from single cells to massive kelp forests. The kinds used for algal turf scrubbers are of the “filamentous” variety and are made of long strings of individual cells strung together and resembling clumps of long, slightly slimy hair.

            So how does algal turf scrubber technology work? Essentially, screens of metal mesh are arranged at a slight angle in a waterway such that a shallow layer of water runs over them. Dense colonies of algae grow on these screens, making them look like very soggy grass “turf.” The turfs are “self-seeding” meaning that the natural algal species that grow best in each environment implant themselves on the screen and us bumbling humans just have to watch. As the water runs over the algae mats, the plants do what plants do best: grow. Conveniently enough, the fuel the algae needs to grow is exactly what we want taken out of the water: inorganic nitrogen, phosphorus, and carbon dioxide. The water then flows off the other side of the algae-coated mesh “scrubbed” of these minerals and injected with dissolved oxygen. This process is especially effective in improving waters contaminated by sewage (treatment plants or farm run-off) and commercial fertilizers. In fact, these systems effectively work to fertilize growing algae with the wastes from our homes and farms.

            And now for the promised, “But Wait, There’s More!” All of this scrubbing and growing ends up producing a lot of algae. In fact, the turfs need to be harvested (by regular old garden variety shop-vac) about once a week to ensure the highest levels of growth. The beautiful thing about this technology is that you can use the produced biomass for more green technology. All of that rich, fertilized turf turns out to make great fertilizer itself, without the environmental baggage of commercial fertilizers. The slimy green harvest can also be fermented to methanol, ethanol, butanol, and methane, all of which can be used as alternatives to fossil fuels at a fraction of the cost of producing the same products from corn or soy.

            One man’s waste-water is another algae’s smorgasbord. By using algae to help clean the waters in everything from streams and rivers to areas of ocean, we can come closer to having our beef and feeding it too.

Friday, 3 June 2011

Why the Minotaur Needed Slime Mold

Photo Credit janthornhill.com
There’s just something about mazes. From PacMan to the hedge-labyrinths of yester-year, a good maze tantalizes the human mind. In fact, the combined esthetics and mental acrobatics of maze negotiation are so inspiring that for decades scientists have been harnessing the power of this puzzle. Yes, our trusty lab coat-clad comrades have tested the “intelligence” of many species using this age-old challenge, ultimately finding that we’re not the only ones capable of corn-maze escape. This prestigious group includes such proto-Einsteins as mice, guinea pigs, octopi, and… slime mold?

            What exactly is a slime mold? This is a harder question than you might think, as classifying these organisms is anything but straightforward. Broadly, they are eukaryotic organisms; like you and I they have a membrane-covered nucleus inside each cell that contains their DNA. Unlike you and I, they are not one organism made of many cells that are each part of a specific tissue (eg. bone, heart, or lung). Instead, they are either single cells or groups of cells that look more or less all the same. To complicate things further, they look vastly different at different points in their life cycle, even switching from life as individual cells to blob-esque communities. The labyrinth-saavy slime molds are in the latter state referred to as plasmodium.

            Although it sounds like something made up by a nineteenth century “psychic,” plasmodium is really an incredibly interesting, gutturally disturbing, and biologically useful body type. While the typical human cell has one set of chromosomes surrounded by one nucleus that is itself enclosed by one cell body, the plasmodium smashes this neat order into something straight out of science fiction. In this form, many cells exist as a community but share a single cell membrane. This means there is free exchange of nutrients and other materials through the goo inside the cell(s) without the inconvenience of actually having to ingest shared materials. This is somewhat akin to everyone in your neighbourhood getting together for a big group hug and then having all your skins fuse together. Although slightly terrifying, this situation has the advantage that only the ones closest to the BBQ have to eat for the whole group to be fed. But wait, there’s more! Due to the pseudo-multicellular nature of plasmodium, you can cut it up into tiny pieces, each of which will terrifyingly regenerate into new, whole healthy beings. Conversely, when two plasmodial slime molds meet they fuse together to form a single, larger plasmodium. The movie possibilities are truly endless.

            So what on earth does this have to do with mazes? The biological advantage of the plasmodium body is that a community can explore different directions while feeding back any nutrients to the rest of the group through tubes made of the cell body itself. The result of this behavior is a tubular complex that navigates the environment by building up the network in the directions of food, and breaking it down in “dead end” directions. Scientists have found that this actively re-optimizing network has properties similar to those used in modern computing, and yes, can be used to navigate mazes. One group is even comparing the patterns of slime mold plasmodium growth with those of roads on the Iberian Peninsula.

            While the research fields of Urban Planning and Microbiology are currently separated by several university blocks, who knows? Maybe some day we’ll be driving highly efficient highway routes first sketched out on Petri dishes rather than engineering pads.