The Random Whale Wiki App - Android

Ever want to just stumple-upon random Cetacean information from Wikipedia? Here is an App for that!  I made it as a fun way to lazily learn about marine mammals on my tablet while in bed: just lie back and learn about the fascinating behaviour, evolution, phylogeny and all the mangled bytes on Wikipedia's Cetacean portal.

Instructions:
> Download the .apk file here
> Move the .apk onto your android device, via bluetooth or usb or whatever. Move it anywhere in the android file structure, but make sure you can find it again within your Android file manager (I use ES File Manager).
> Detach fron computer and turn on your Android. Browse to the .apk file and tab. Follow instructions to install!
> To locate the Random Whale Wiki icon, you'll need to manually drag it onto your 'desktop' through Settings--> Apps.

The app is admittedly primitive: just a refresh button to get a new marine mammal article, plus some facilities for directed browsing. Enjoy! The real engine is the Wikipedia Random project.

Personally, I think Wikipedia is great for learning about science. Recent innovations like the organized Portals are downright exciting! I like the Biology Portal. Who would want the linear bore of an intro college textbook, when you can have the organic cluster of articles that allow you to click-through and venture out into the Wikispace as far as you are willing to go?  Just be mindful of Wikipedia's biases and reliability.

Are you a fan of Wikipedia random-browsing? How do you use the web's 2.0 resources for edutainment?

Christmas bird Count -- Mayhem birding

Having returned from point counting birds in the tropics, the annual Christmas Bird Count is comparatively quite fun for all its quirky opposites to the speciose, song-rich, in-tune-with-nature sport of spring or summer. I did mine inland of Port Rowan, Southern Ontario, hiking around in silent, snowy weather, in lame pursuit of the very few winter species and lost aberrants who tough it out in the dark, cold, frozen landscape. What better way to celebrate the holy Winter Solstice, than to defy life-in-hibernation, and work hard to get what you want from Nature: stomping through icy wetlands, crashing through brush, scaring up what we could, and invading people's bird feeders to stack the count – mayhem that counts as a count, opposed to the disciplined, randomized, systematicitized, protocolized summer studies.

37 species in all, a count that was well earned for 8 hours in the cold. 103 species in total for the Port Rowan area. Christmas just took on a whole new wholesome meaning for me!


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Development practitioner -- a bridge between worlds

This spring and summer, I’ve had a coveted placement through the Canadian International Development Agency (CIDA) to practice sustainable development in a little known archipelago in the Southern Antilles. Known to the wider public as the tropical backdrop in Pirates of the Caribbean, the small island nation of St. Vincent & the Grenadines has lured many foreigners to its shores, from international organizations, wealthy Hollywood types, to coastal resource
developers. The fascination may be due to islands’ remoteness along the Southern Antilles chain, leaving it relatively unscathed by the environmental despoliation so common in the more colonial North. Here, foreigners come and fall in love with a glimpse of beaches, reefs, and mountains of a Caribbean that once was.

The attention has not always been beneficial, however, and it is in this context of suspicion, grudges, and hope which has shaped my placement and provided the most insights into sustainable development. The worst examples of foreign development blight the seascape in ruin, such as a foreign company’s failed marina project near Ashton, on  Union Island, where I lived. Despite a damning environmental impact assessment, the company slashed through Mangrove, dredged up coral, and constructed a long causeway of steel pilings and concrete, only to go bankrupt and leave the lagoon in devastation. The abandoned causeway has blocked tidal flushing of the lagoon, killing off most coral and conch, leaving stinky stagnant water, and stunting the growth of the nearby mangrove forest.

Enter myself: a youthful ornithologist from the Coady International Institute on a six month placement. I’ve been charged with setting up an ecosystem monitoring regime for the lagoon, as a restoration project attempts to reestablish the tidal flushing (funded by a US
grant through the Neotropical Migratory Bird Conservation Act). In this, I’ve had perhaps the paradise job: wading in hipboats through mangrove forests, recording sightings of rare exotic birds, taking water quality samples along emerald blue coastlines, and writing bird
identification software to train local persons. What could be better than working for the common good, learning a new culture, and living on an Island paradise? Such is the allure of young persons all across Canada enrolling into the Development field.

If it seems too good to be true, it is. This development model of parachuting in a foreign person to solve other peoples’ problems has long been suspect. Despite good intentions, money, and the willingness to work hard, nothing lasting will happen without local persons firmly in the driver’s seat. This came to lightly lividly as one of my CIDA-funded colleagues had to be pulled back from a Grenadine Marine Protected Area, arguably fighting the good fight for principles of environmental sustainability and community control, but doing so with too much initiative and not enough local oversight. My predecessor was brought to tears as a local organization lambasted her organization for being too controlling and arbitrary with funding. In contrast, a third organization charged us with being too lax about finances, ceding too much control to a local strongman, who then spirited away the funding. Such is the knife edge of participatory development: on the one hand, people are sensitive to the faintest whiff of paternalistic control by foreigners, and on the other hand, there is sadly an all-too-real risk of “take the money and run” in the majority world.

These lessons come late, but I may have stumbled into a way forward while struggling with a macroalgae mariculture cooperative, who had its own negative history with development NGOs. Initially frustrated with lost data and things not getting done, the slow pace allowed me time to absorb Island culture and build relationships with community groups. This culminated in a “baptism by fire” airing of grievances which paved the way for frank discussions and genuine friendships. Relationships are everything on Union Island, both as a way “in” to get things moving, and as the glue which governs people’s sense of responsibility. We’ve since won funding through the United Nations Development Programme’s Global Environmental Facility, to start capacity building and environmental monitoring.

Through the Coady International Institute Youth-In-Partnership Program, I’ve come to see international development as being about building bridges—linking the highly technical and micro-managed world of donor organizations with the realities of working on-the-ground in places abroad. Young persons interested in pursuing a life in development need to be able to listen, be likeable, and be able to straddle two worlds fluently.

Genome not as useless as previously thought (was there any doubt?)

I had written earlier that only 4% of the human genome actually codes for proteins, relegating the rest to “junk DNA”. This is only partly true, at least according to a new study in Nature by Dr. Laura Poliseno et al, which suggests that approximately 40% plays a physical, regulatory role.

While many biologists tentatively accepted the 96%-junk-DNA figure, persuaded that the vast amount of parasitism at the organismal level could be mirrored at the DNA level, the concept has been quite unsettling. Poliseno’s hypothesis returns some sanity to our most fundamental unit of self.

According to Poliseno and team, plenty of the junkish pseudo-genes resemble other protein-coding genes, just enough that they attract and bind to floating bits of complimentary micro-RNA. The soup of complimentary DNA snippets would otherwise bind to the gene proper, and hinder the normal protein-producing machinery, thereby down-regulating the proper gene’s expression. He tested this idea using the PTEN tumour suppressor gene and its pseudogene PTENP1.

While knocking down one tenet, it does promote another—that gene expression is a complex, graded process, with nuances and interactions with the environment, that make any sort of one-to-one mapping of genome-to-phenotype, incredibly difficult.

However, this study does not entirely vindicate the genome as some well-ordered, perfectly designed recipe. 40% still leaves a lot of unexplained DNA. One of the more interesting bits are the LINE-1’s (which I wrote about in You are descended from Viruses) making up 20% of our genome, and seem to come from retroviruses, being good for nothing else but replicating and reinserting themselves in our genome.

Or are they? Dr. Gage noticed that LINE1s were more active in the brain tissue of developing mice than in other parts. He admits that they do not code for anything and really are just a random self-replicating nuisance. But could natural selection have taken advantage of such randomness as a beneficial process unto itself? Gage (GAYJuh) points out that developing brains a) have much more active LINE1s then other tissue, and b) they are over-resourced, with an initially superfluous number of neurons and connections which mostly deteriorate with age, leaving the core synapses for the more mature brain. Gage suggests that this deterioration is a sort of “survival of the fittest” of cells whose genes have been scrambled up by hyper-active LINE1s. Mostly, the random insertions of LINE1s will lead to neutral rearrangements, but sometimes they’ll disrupt another gene, and perhaps they may have a beneficial effect, and these he suggests are ones which survive to maturity.

Such a process occurs entirely in somatic cells, and is not passed on through gametes to the next generation. Rather, it is a sort of micro-natural selection that promotes an optimized network within a developing individual. Its an intriguing suggestion, and harkens suspiciously to the idea that complex networks themselves beget consciousness—an idea which is being explored more in computer science and problem solving, as in artificial neural networks.

Whether this study hypothesis bares out in the long run, it does suggest more scrutiny should be paid to the role of viruses in evolution and development. They are, after all, the most distilled essence of life possible.

Connections across the planet, off a different sort

It is not long after you’ve been birdwatching that your mind starts to expand to far off continents, high-elevation weather systems, and genomic machinations. What contrivance of weather, bad luck, and instinctual migratory clockwork colluded to drop so many new visitors to the salt ponds and mangroves of Union Island? Today, we were startled to the mangroves crowded with the a flock of juvenile Forktailed Flycatchers (Tyrannus savanna). Gone were most of the frisky Lesser Yellowlegs (Tringa flavipes) and breeding Spotted Sandpipers (Actitis macularius) which cluttered the Ashton saltponds just days ago. Even some of the more reclusive locals, like the Smooth-Billed Ani, the Green Heron, and the Mangrove Cuckoo, also made especially impressive turnouts at the suburban ecosystem.

Such delightful variation standout in contrast to the neat and clean distribution maps printed in birding books. The Lesser Yellowlegs, for example, spends late June and July breeding in the tundra of Canada and Alaska. However, one can easily go to eBird.org, and produce a map of sightings over the entire Western Hemisphere during July. Rather than being confined to the Arctic, sightings of Yellowlegs speckle the Caribbean and North America in the thousands. Mostly, they are the (welcomed) losers: a lost lover, a predated nest, a freak arctic storm, there are so many ways that individuals fail to breed and instead gang up in early southbound flocks to entertain birders.

What started out as a great day turned far, far worse. I went to the office today to discover we'd been evicted! Such are the realities of working in a place where politics and bureaucracy are too intertwined. Stand out, and you will be quashed down.

Endemic species: a rare encounter on Union Island

The Union Island Environmental Attackers Bird Watching crew had a rare find today while hiking along the eco-trail above Chattam Bay, on the Western uninhabited portion of the Island. The humid forest with its craggy boulders is the only known location of a tiny, blue-spotted gecko, Gonatodes daudini, which is endemic to Union Island. The Attackers were lucky enough to spot the rare creature hidden in a narrow, crevice along the trail. They join the ranks of only a few dozen humans to have ever seen daudini.

Little is known about the tiny gecko, which was just described in 2005 after a discovery by Mark De Silva. With hard work, proper planning, and good luck, Union Island may be able to protect the one-of-kind gecko, and its unique forest-- a veritable Gem in the Grenadines. While the lizard and forest may not be a major attraction themselves, the key would be to link the disparate attractions together as a markable eco-tourism package: from bird-watching in Ashton Lagoon Mangrove, Salt from the Belmont Pond, turtle patrols in Bloody Bay, and forest ecology and endemic species along the once-maintained eco-trail. Union Island has plenty to offer visitors.

The Sustainable Grenadine Inc’s recently approved Ashton Lagoon Restoration Project will facilitate a tourism steering committee to orchestrate such a linked-up package, while another proposal is in the works for the National Trust.

Myself having seen the Island’s endemic species, can rest a bit more satisfied, having been involved with most of the islands more valuable natural systems. I’ve only a couple months left here, and too much work to do. I hope that others can carry the torch when I leave.

(Photo by Union Island Environmental Attacker, Stanton Gomes)

Entropy and biodiversity: contradictory tendencies?

A reading of Vlatko Vedral’s Decoding Reality, a treatise on the physical nature of information and it’s roll in just about everything, gives a novel spin on an old question in evolution: is there a natural tendency for life to increase in complexity and biodiversity? There have been arguments for and against this idea.

Some science heavy-weights, like the late Stephen Gould, suggested an opposite trend. He viewed the fantastical array of morphology and extinct taxa in the Cambrian-period (some 530 mya) as revealed by Burgess Shale fossils, as evidence that diversity has in fact decreased. It seemed that most modern phyla appeared early on in Earth's history, and we've since lost many of the most bizarre taxa. (The Fossils were so weird looking that early discovers gave new taxa names such as Hallucigenia. Researcher Simon Conway Morris is said to have opened a box of fossils to exclaim, “oh fuck, not another new phylum!”) The suggestion was that the greatest variety of life existed early on, and has since gone through a winnowing process.


Hallucigenia sparsa, an extinct animal from the Cambrian Period

However, more recent assessments of the Burgess Shales, and literal rearrangements of body parts, suggests that the past wasn't so weird, and many of the Cambrian freaks are actually related to modern extant phyla. Furthermore, most quantifications on the complexity of life, such as the number of fossil species plotted over time, show an unambiguous upward trend (despite ~6 mass-extinction events).
Philosophers have also weighed in on the question of Life’s increasing complexity, and done so from some fairly basic principles, such as the Second Law of Thermodynamics, or Entropy, the tendency for a closed system to go from organized to disorganized. For example, hot and cold want to equalize, great artworks weather and fade, litter scatters in the wind, and my desktop gets more cluttered.

Life seems pretty miraculous when compared to this Fundamental law. It seems that most creatures are hell bent on moving matter around into orderly patterns. Arguably, a basic definition for Life may be the maintenance and control of orderly gradients over membranes, which otherwise want to equalize and lose their dynamism. Your very neurons are in fact just changes in concentration gradients of K+, Cl-, and Ca2+: the brain demands a lot of energy to do so, consuming 25% of a human's glucose.

Vedral offers an interesting take on this seeming contradiction between the Universal law of Dissorderliness, and Life’s tendency to increase in complexity. He does it by linking Entropy with Information, the key that both have the same basic equation, thanks to Claude Shannon's work at the Bell Labs during the 1940’s. The information content of a phenomenon is the log of how probable the event is. This is both physical and intuitive. Consider the News: a report on an Icelandic Volcano eruption downing all European air-traffic is more news-worthy (and informative) than a report on a regular traffic congestion. One has a much lower probability of occurring than the other, and therefore its occurrence is informative.

Information, therefore, is inversely related to the probability of something happening, and has the same functional form as Entropy, the tendency for low-probability states to decay into more probably states (e.g., a clean room goes from organized to disorganized--the reverse being highly unlikely to happen on its own).
The information analogy finds obvious utility in genetics. Considering the phenotypic output of our genes--you’d guess that the genome is a highly ordered thing-- and thereby existing in a highly improbable, low entropy state. How the heck could something so ordered and useful come about naturally, when disorganization is the rule of the universe?

Enter entropy, manifesting as random mutations. Our cellular machinery employs considerable energy checking and repairing such mutations. Cancer is one consequence of the failure to do so. But at the same time, these mutations are key to natural selection: every so often, a beneficial mutation occurs and increases the heritable variation within a gene pool, thereby giving natural selection something to “select” upon. Entropy breeds variation! Think of it another way: it would be a highly improbable, extremely low-entropy affair if our cellular machines could replicate themselves perfectly and produce vast populations of identical individuals ad infinitum. Such a state of affairs is just begging for a lesson in thermodynamics.

(The “beneficial” variation also comes with an immense amount of “junk” variation too. Previously, it was thought that only 4% of a human’s genome actually does anything useful. This number has been recently bumped up to 44%-- nonetheless, that is still a lot of “junk” within the our precious Codebook for Life)

“Endless forms most beautiful” as Darwin wrote, and that’s what we have to look forward because of the degenerative tendency of the universe.