22 May 2016: Crows got smarts


Corvus corax, the common raven. Photo: Pkspks [CC BY-SA 4.0]

It’s no secret that corvids – crows and ravens – are exceptionally smart for birds, especially at problem solving. Now an experiment carried out with ravens provides evidence they may have a basic Theory of Mind as well; this means they have an ability to attribute mental states they experience to another raven.

In a paper published in Nature in February, researchers Thomas Bugnyar, Stephan Reber and Cameron Buckner from the universities of Vienna and Houston, carried out an ingenious experiment that tested how ravens caching food behaved when they thought they were being seen by another raven.

There is increasing evidence that the Theory of Mind exists in chimpanzees, bonobos, scrub jays and ravens. How equivalent the experience of a ToM is between species is, so far, untestable, but the strong possibility that some form of ToM exists in different animals provides yet more evidence of the complexity of the mental life of species apart from humans.

Not only does this add weight to calls that humans should reconsider the way they relate to other animals, especially the often appalling way we treat farmed and domesticated animals, but firmly places Homo sapiens as the product of the same evolutionary process that produced ravens, dogs and garden slugs.

04 September 2015: Neither one thing nor the other

P. myojinensis

P. myojinensis. The blue structure is the nucleus, the red structures the endosymbionts.

A remarkable creature discovered in the ocean southeast of Japan – that doesn’t quite seem to belong to any of the three known domains – may provide evidence of how complex multicellular life evolved on Earth.

In 2010, a scientific expedition to the Myojin Knoll, about 35 kilometres southeast of the Japanese island of Aogashima, collected biological samples from a hydrothermal vent more than 1,200 metres below the surface.

The samples were frozen and then embedded in epoxy resin; the resin was then prepared for study by being sliced into ultrathin sections.

That’s when the researchers discovered they had collected one truly remarkable specimen, a single-celled organism that lays somewhere between prokaryotes, organisms like bacteria and archaea, and eukaryotes, the basis of complex organisms such as fungi, plants and … well … us.

The main differences between prokaryotes and eukaryotes are that the former do not have a nucleus surrounded by a membrane, or any membrane-bound organelles such as mitochondria or chloroplasts.

As described in the journal Microscopy, the cell, dubbed Parakaryon myojinensis, was discovered on one of the bristles of a type of Polychaete called a scale worm. It was 10 micrometres long and three wide, much larger than most bacteria. Inside the cell the researchers discovered a nucleus with a membrane. As well, they discovered three endosymbionts, organisms that live symbiotically inside another, also surrounded by membranes. Obviously, then, the cell was not a prokaryote.

However, the nucleus of P. myojinensis was surrounded by a single membrane and consisted of DNA fibres, whereas a nucleus in a eukaryote cell has a double membrane and consists of chromosomes.

The endosymbionts also had only a single membrane. Mitochondria in eukaryotes, like the nucleus, have a double cell wall. As well, the endosymbionts closely resembled bacteria rather than mitochondria.

This last point is what makes the discovery of P. myojinensis so important.

There are two major theories about how eukaryotes evolved. The autogenesis theory proposes that a eukaryote’s structures developed from primitive prokaryotic features. The symbiogenesis theory – first properly described by Russian Konstantin Mereschkowski in 1910 and subsequently advanced by Lynn Margulis in 1967 – proposes that eukaryotes evolved from a symbiotic relationship after a bacteria was absorbed by larger achaean, eventually becoming an integral and working part of the cell.

P. myojinensis seems to be an organism that has incorporated endosymbionts into its structure but not yet developed the full range of eukaryotic functions.

As the authors of the paper suggest, “ … it may even be a conservative descendant of the transitional lineage between prokaryotes and eukaryotes.”

For a fuller description of the possible implications of the discovery, read this article on ABC online by British scientist Nick Lane, whose latest book The Vital Question: Why is life the way it is?, is a rewarding and thought-provoking read.

20 August 2015: Shine on Pluto


Pluto as seen by New Horizons. Image credit: NASA/JHUAPL/SwRI

AJ and I ducked out of the house on the night of August 11 to have a quick wine or two at King O’Malley’s pub in the city. When we got there we discovered the place had been invaded by Science in the Pub, and the two of us spent a pleasant hour drinking white wine, eating free food, and watching a slide show about the New Horizons mission to Pluto.

What’s more, it was a presentation hosted by John Berry, the American ambassador to Australia, and featured Nobel prize winner Brian Schmidt from the ANU, science communicator and astrophysicist Alan Duffy from Swinburne University of Technology, and Glen Nagle, Education and Outreach Manager at Canberra’s Deep Space Communication Complex at Tidbinbilla.

It was a pretty crowded affair and the screen was sometimes obscured by jostling customers, excited science addicts and through-traffic, but the mood was positive and the atmosphere … well … sciencey. (If this isn’t a word already, I bag naming rights.)

What follows are some of the amazing facts we learned about the New Horizons mission and Pluto, plus a few extra tidbits.

The mission was launched on 19 January 2006, when Pluto was still classified as a planet. Eight months later it was demoted to a dwarf planet. Furthermore, in 2006 only three moons had been identified orbiting Pluto. Before the probe reached its destination, we knew of five moons.

The probe’s closest approach to Pluto occurred nearly nine months after launch, on 14 July 2015, and after a journey of approximately 7.5 billion kilometres. Disappointingly, New Horizons was 7.5 seconds late for its appointment.

Still, not too bad when you consider that to travel the same distance travelling at a highway speed of 100 kph, it would take you around 8,560 years. In other words, to arrive in 2015 you would have had to start driving about the same time the world’s first city walls were being built around Jericho.

Shots of Pluto’s night side were made possible because of reflected sunlight from Pluto’s largest moon, Charon.

Pluto’s atmosphere expands as its eccentric orbit brings it closer to the sun, and then freezes when Pluto recedes from the sun. Since its last closest approach to the sun in the 1990s, Pluto’s atmosphere has halved. This was confirmed by a radio signal sent from Earth to New Horizons through the atmosphere when the probe reached the other side of Pluto. The signal had to hit a piece of equipment about the size of a credit card, and enabled scientists to measure the signal’s radio occultation.

Scientists were surprised to discover that ultraviolet light broke up some of the methane in Pluto’s atmosphere create more complex hydrocarbons such as ethylene and acetylene. They were even more surprised to learn that about 50% of this UV comes not from our sun, but from other stars.

Pretty exciting stuff for a dwarf planet.

All in all, an excellent night at the pub.

19 November 2014: AI not a threat

It’s remotely possible that an AI already exists, burbling away quite happily and innocently somewhere on the Internet, ignorant of the miracle of its own existence and no more self-aware than a box of tissues.

The possibility that it’s plotting the destruction of humanity, let alone all life on Earth, seems remarkably unlikely. It may not even realise in any logical sense that there is such a thing as biological life.

And if its intelligence was to develop self-awareness (a big ask) and subsequently an awareness that other life exists (another big ask), so what? Why would it divert resources away from sorting through key words for the NSA (or whatever task it was created to fulfil) to devise some method of eliminating humanity? What broken thread of logic would set it on such an absurd course?

But what if an AI accidentally sets off Armageddon?

In an article for the New York Times titled “Artificial Intelligence as a Threat”[i], technology writer Nick Bilton raises the possibility of a “rogue computer” derailing the stock market, or a robot programmed to fight cancer concluding “that the best way to obliterate cancer is to exterminate humans who are genetically prone to the disease.”

Well, hell, why not go the whole hog and create an AI that can both derail the stock market and exterminate humanity?

In both of these scenarios, surely AI is at best an option? I can imagine a plain old stupid robot making both of these mistakes because of crappy programming or intentional sabotage. Neither case is a genuine argument for we old-fashioned biological intelligences to be afraid of AI. (They may, however, be arguments for us to be afraid of important decision-making being taken from human hands and put into the silicon hands of machines that don’t give a damn, whether or not their processors amount to real intelligence or just a hill of beans.)

Bilton then raised the possibility of self-replicating nanobots being programmed by someone of “malicious intent” to extinguish humanity. But again, the nanobots don’t have to possess AI for this nightmare to become a reality.

Bilton concludes with two possible problems with AIs put forward by futurists like Elon Musk. First, that AIs created to make decisions like humans will not have a sense of morality, and second, that intelligent machines will one day go on to build even more intelligent machines that ultimately will lord it over the planet.

While it is true that AIs are unlikely to have a sense of morality, they are no more likely to experience murderous paranoia, or indulge in sociopathic tendencies. A human without any morality may want to kill other humans, but how does that translate to an AI without morality wanting to kill humans, or for that matter kill other AIs?

As for AIs creating super-AIs that end up ruling the earth, why would they want to? I love playing Civilization V on my computer, and using my tanks and political clout to take over the whole game map, but if I had a brain the size of the Empire State Building there’s about a zillion other things I could do that would keep me entertained and fulfilled, and none of them involve bending creatures of lesser intelligence to my will. There’s a whole universe out there to explore, and telling the Simon Browns of this world what to do or how to do it simply wouldn’t float my chip.

[i] And three days later picked up by the Sydney Morning Herald for its weekend edition of 8-9 November 2014, which is where I came across it.

02 November 2014: But I discovered the meaning of life!

Who’d have thought that in a competition between scientific research papers on the wonders of sex, the bizarre mini-universe of quantum physics, the age and size of the cosmos, the last universal common ancestor, the wingspan of giant condors and the implications of relativity, the top three most cited papers would be about proteins?

The most recent issue of Nature, one of the world’s leading academic journals, has a fascinating article about the most popular papers in science.

The top three – and here you need to take a very deep breath – are “Protein measurement with the folin phenol reagent” (1951), “Cleavage of structural proteins during the assembly of head of the bacteriophage T4” (1970), and “A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principles of protein-dye binding” (1976).

I didn’t even know “quantitation” was a word, let alone part of the title of a scientific articles that has over 150,000 citations.

For the full wherefore and whyfore, go read the article. In the end, as it generally does in science, it all makes sense.