An octopus enrichment handbook

Athena’s suckers felt like an alien’s kiss—at once a probe and a caress. Although an octopus can taste with all of its skin, in the suckers both taste and touch are exquisitely developed. Athena was tasting me and feeling me at once, knowing my skin, and possibly the blood and bone beneath, in a way I could never fathom.

-- Sy Montgomery

Rhino gone

Poaching has driven the Javan rhinoceros to extinction in Vietnam, leaving the critically endangered species' only remaining population numbering less than 50 on the Indonesian island that gave it its name, the WWF and International Rhino Foundation said on Tuesday. "The last Javan rhino in Vietnam has gone," said Tran Thi Minh Hien, WWF-Vietnam country director. "It is painful that despite significant investment in the Vietnamese rhino population, conservation efforts failed to save this unique animal. Vietnam has lost part of its natural heritage."

-- report

Oncos

Cancer stem cells have acquired the behavior of normal stem cells by activating the same genes and pathways that make normal stem cells immortal -- except, unlike normal stem cells, they can not be lulled back into physiological sleep. Cancer, then, is quite literally, trying to emulate a regenerating organ -- or, perhaps, more disturbingly, the regenerating organism. Its quest for immortality mirrors our own quest, a quest buried in our embryos and in the renewal of our organs. Someday, if a cancer succeeds, it will produce a far more perfect being than its host -- imbued with immortality and the drive to proliferate.

--- from The Emperor of All Maladies by Siddhartha Mukherjee

C.S.I.: Dog Dump

‘Globally endangered Egyptian vulture!’ shouted Çağan, slamming on the brakes. Glancing skyward, I caught a glimpse of something brown flapping away. The body of the Egyptian vulture is brown and off-white, but its face is bright yellow. ‘They get that colour from eating shit, which is full of yellow carotenoid pigments,’ Çağan explained. In males, the bright-yellow face is an indicator of fitness and virility, signaling a capacity to eat enormous quantities of shit without getting sick.

On behalf of the Egyptian vulture, as well as the region’s other vulture species Çağan had recently opened a ‘vulture restaurant’...which in its pilot phase had served mostly dead dog. Emrah, Çağan’s science coordinator, was charged with retrieving dog carcasses from the city dumps and depositing them in random locations around Aras, to see how the vultures reacted. The vultures reacted well. You bring the dead dog, and the vultures take care of the rest. The one problem was that a lot of dogs in the dumps had been poisoned as part of a stray-dog reduction program.

...Thus began a phase of Emrah’s life that might have been called “C.S.I.: Dog Dump”: did this dog die of natural causes, or was it poisoned? He started out bribing the staff at the dumps, a pack of cigarettes for every clean carcass. It was a good system, although Emrah inevitably began asking himself certain questions. Was it for this that he had completed his master’s in biology? Further, the workers at the dump clearly thought he was some kind of pervert. One of them once remarked that Emrah might not find that day’s dog suitable: “The thing is, this one is male.”

-- from Natural Histories: A journey in the shadow of Ararat by Elif Batuman

The waltzing kludge of eukaryotic life

At its heart, [the idea] is deceptively simple: we have two genomes that need to work together, and you can tell how well they’re doing this by the strength of the free radical leak. From that simple concept, you can logically derive how fitness, fertility and lifespan are linked in different species. You can also predict the process of ageing and the onset of age-related diseases within individuals. 

“A lot of this has to be true on logical grounds,” says Nick Lane. “We know that there is co-adaptation between these two genomes and many predictions emerge seamlessly from some simple reflections on that process. The big question is whether it’s important in the greater scheme of things.”

-- from The two-genome waltz: how the threat of mismatched partners shapes complex life by Ed Yong

Megavirus

Its genome is 1.259 million base pairs long, which is 6.5 percent longer than the previous record holder among giant viruses. In that abundance of DNA are 1120 genes. That’s hundreds more genes than found in a lot of bacteria.

-- Carl Zimmer on a the world's most ginormous virus.

Some have even argued that they represent a new domain of life, although others aren’t so sure, Zimmer notes.

Jean-Michel Claverie, who discovered it, says the fact that it shares cell-like genes with the mimivirus is 'definitive proof' of a cellular ancestor.

Future fish

The construct also contains a stretch of DNA from the promoter region of an ocean pout, an eel-like creature that lives in extremely cold environments (the promoter is a switch that controls the expression of a downstream gene). Normally, the eel uses this promoter to keep an antifreeze gene turned on constantly so it does not freeze. The promoter is therefore “constitutive,” meaning it is always active, and coupling it with a growth factor gene in an Atlantic salmon results in the salmon experiencing a continual growth spurt—since the growth factor is continually produced. Studies have shown that the genetically-altered Atlantic salmon’s appetite would make it constantly ravenous, meaning that it would eat everything around in sight.

-- FDA Decision Will Lead To First Ever Genetically-Modified Animal For Consumption

Giant killer squid of the Triassic?

We hypothesize that the shonisaurs were killed and carried to the site by an enormous Triassic cephalopod, a 'kraken,' with estimated length of approximately 30 m, twice that of the modern Colossal Squid

-- from here.

P Z Myers is sceptical :

This 'Triassic kraken' has not been found; no fossils, no remains at all, no evidence of its existence. It is postulated to have been large enough to hunt and kill ichthyosaurs, which is remarkable—comparison to modern giant squid is invalid, since they are prey, not predator.

P.S. 11 Oct: Microecos has some fun, but Nature does not dismiss the idea out of hand.

Weed world

What I’m really proposing is a shift in our value system. What we value and don’t value can change. "Weedy" is an interesting cultural concept -- in reality, weeds are successful plants. We should celebrate them, because they’re the plants we don’t have to worry about it. They’re gong to be fine. They’re the resilient part of nature.

-- Emma Marris.

In Solar, Ian McEwan's anti-hero Michael Beard tell his girlfriend that the humblest weed in a pavement crack contains a precious secret (the true nature of photosynthesis) that the world's top laboratories are only beginning to understand.

Cultural transmission in chimpanzees

Trasmisión cultural entre primates from Proyecto Gran Simio on Vimeo.

In Tai National Part, Ivory Coast, a young chimp observes and learns from its mother how to use tools to break open nuts. The film was taken by Serge Soiret of the Great Ape Project.

Jelly world

Hyperbole?

a future 'gelatinous' ocean reminiscent of the early Ediacaran if fishing and other anthropogenic stressors remain unchanged

-- from Faking Giants... Some jellyfish are increasing the amount of water in their bodies in order to increase their size and so collide with more prey.

Life entangled

A useful overview article of developments in quantum biology here summarizes recent research into possible roles in smell, photosynthesis and vision.

Humans have 400 differently shaped smell receptors but can recognize 100,000 smells. Whether a quantum effect (electron tunneling) plays a role remains a matter of speculation.

Metamorphosis: bifurcated being

The larva of Luidia sarsi is a semi-transparent diaphanous sprite that feeds on algae and grows to a remarkable 4 centimetres. Then something extraordinary happens. Instead of changing shape to become an adult, a cluster of cells lining the larva's internal cavity grows, like an alien invader, and out of these a starfish is born. Floating free from its other self, the adult form settles on the ocean floor, where it survives and grows by hunting down other starfish in the dark of night. Meanwhile, the larva continues its vegetarian existence, grazing the surface waters above.

-- from Evolution's freak factory, in which Frank Ryan suggests hybridisation played a role in Cambrian explosion.

See also: Hybrids, chimeras, trees and webs

P.S. In a highly critical review of Ryan's book Metamorphosis, Josh Trapani says that Ryan champions the views of Donald Williamson who postlated that interbreeding occurs between not just different species but different phuyla; for example, between ascidians (sea squirts) and echinoderms (sea urchins):

He postulates that this has happened repeatedly between different groups of widely divergent organisms. Moreover, he postulates that the hybrids look like one parental species as larvae and like the other as adults, rather than simply exhibiting a mix of characteristics, as most hybrids do. Not only is this hypothesis not supported by evidence, but plenty of evidence, including powerful molecular evidence, directly contradicts it.

A monster's heartblood

There was once a monster which lived in the valley of the Clearwater River near Kamiah. This beast devoured all the animals that lived in the country for miles around and became such a menace that Coyote...decided it must be killed. Arming himself with a flint knife, he jumped down the animal's throat and stabbed it in the heart. Then he cut the body up into pieces and from them fashioned tribes of Indians which he sent to occupy the mountains and plains round about. Finally, he discovered that he did not have a tribe for the beautiful valley in which the monster had lived, so he squeezed a few drops of blood from the heart and from this made the Nez Perce. Thus from the lifeblood of this strange animal came a tribe having many of the most admirable qualities possessed by human beings.

-- Nez Perce origin story via The Flight of the Nez Perce by Mark Brown (1971) via Wikipedia.

'New dances with wolves'

In a talk advocating the reintroduction of wolves to Scotland, Jim Crumley quotes Doug Smith, the head of the Yellowstone wolf reintroduction project since it began in 1995:

Clearly this is an animal less likely to offer scientists irrefutable facts than to lure us on a long and crooked journey of learning.

Uunartoq Qeqertaq

One here for the Nuvvuagittuq Eidouranion (a phrase to be explained another time):

According to the Times Comprehensive Atlas of the World, Greenland lost around 15% of its ice cover between the 10th edition (1999) (left) and 13th edition (2011) (right).

Uunartoq Qeqertaq – translated from Inuit as Warming Island – joins Southern Sudan and nearly 7,000 other countries and places added or changed since the last edition of the Times Comprehensive Atlas of the World.

The Greenland ice sheet is said to have shrunk by about 15% in 20 years. Update 19 Sep: the 15% figure is said to be an exaggeration. [1] (See This is what global warming looks like.) Where, exactly things go from here, and when, is hard to predict. The ice sheet may not disappear as quickly as some previous models have suggested. (The precise impacts of fresh and seawater ice melting are also unpredictable.)

But in the absence of dramatic changes in the nature and pattern of human activity, the likely trend is towards complete disappearance of the ice sheet. In a review of Deep Future: The Next 100,000 Years of Life on Earth by Curt Stager, Scott L. Wing writes:

Relying on simulations of the effects of high partial pressure of carbon dioxide by Richard Alley, Jeff Ridley, and others, Stager lays out the development of Greenland's landscape and economy as its ice cap melts. He even playfully proposes a name, Ny Fjord (New Fjord), for the giant tongue of ocean that could come to occupy central Greenland by 5000 CE. He envisions a thriving Arctic-fishing industry lining the shores of the 400-m-deep fjord, then explains how the fjord would (to the shock of most nongeologists) empty over the succeeding 50,000 years as isostatic rebound following deglaciation raises the crust of central Greenland. 

Footnote

[1] (added 21 Sep): see Greenland Meltdown at Realclimate.

Man and animal

What birds and animals offer us is not confirmation of our sense of having an exalted place in some sort of cosmic hierarchy. It's admission into a larger scheme of things, where our minds are no longer turned in on themselves.

-- John Gray.  Irony apart, a better appreciation of birds and animals might help in the era of 'post-whateverism.'

Invasion of the fungal body stranglers

Imagine if a tree could lasso your body as you run past. That’s pretty much what some nematophagous fungi (and Vampyrellid protists) do in soils—capturing (very) motile nematodes, suspending their motion, and digesting them whole. Some fungi entwine nematodes with their rope-like hyphae and choke the poor worms to death. Other fungi inject their roots into a living worm, sucking out nutrients and killing the nematode as the fungal mass grows. (As another strategy, Vampyrellid amobae engulf nemtodes whole in a blob of goo.) To top it all off, nematophagous fungi unleash siren-like powers (perhaps by emitting sensual chemicals scents?) that attract unknowing, healthy nematodes towards their webs.

-- belatedly, from Marine Fungi are Totally Badass at Deep Sea News

Adventures in rhino stimulation

Following a table of typology, definitions and potential agency of extinction terms as outlined by Richard Ladle and Paul Jepson, the white rhino is, presumably, on the point of crossing from the status of 'Ecological extinction' to 'Phoenix extinction.'

Two recent developments may help it from slipping into total extinction: the conversion of its skin cells into pluripotent stem cells, and electroejaculation with a uniquely designed probe.

'First there was an island -- then there was a boat'

What draws me to these places is hard to define. The journey is part of the magic. The sea is endlessly, and wonderfully alive; unlike concrete, unlike tarmacadam. No two sea journeys are ever the same. On the trip to North Rona, we met families of dolphin, Risso’s, basking sharks and minke whales. The sea was calm, the swell long and leaden. The night-time journey back was before a north-easterly gale, sailing only on the jib. Driving southwards at eight to ten knots, we listened to the clicking of a school of pilot whales some three miles away.

-- John Cumming, Cape Farewell