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.