Science

14 December 2017: Colin Groves (24 June 1942 – 30 November 2017)

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My friend Colin Groves died two weeks ago this day. It came a surprise, although I knew he was in palliative care. He seemed invincible as those with a great intellect always seems invincible, as if death could be put off indefinitely. Although aged he was never an old, and although physically ill his mind was as sharp as an Acheulean hand-axe.

In a real sense his work makes him immortal, at least as far as any human can be immortal. I knew him chiefly as a friend and fellow skeptic, and more recently as a co-writer. Although I had some knowledge of his standing among taxonomists, anatomists, biological anthropologists, primatologists and palaeontologists, he was overwhelmingly modest. Just the preceding list of fields should give you some idea of the breadth of his knowledge.

When Jane Goodall was asked what it felt like to be the world’s foremost primatologist, she replied ‘You’re mistaken. The world’s foremost primatologist is Colin Groves.‘[i]

At his funeral, colleague Professor Kristofer Helgen noted that Colin had named more than 50 new kinds of mammals, and that the first, the Bornean Rhino, remains the largest living mammal described in recent generations.[ii]

‘Colin was the most influential large-mammal taxonomist of the last half-century. His discoveries and impacts are astonishing … The last species he named, in a paper which appeared … in the last month of his life, was the Tapanuli orangutan, one of only eight living great apes on our planet … ‘

As Professor Helgen points out, Colin is probably best known for describing Homo ergaster in 1975, together with Vratislav Mazák. Homo ergaster, which lived in Africa between 1.4 and 1.9 mya, was probably one of our direct ancestors.

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Homo ergaster. ANU cast of cranium KNM ER 3733, discovered at Koobi Fora, Kenya, in 1975 by Bernard Ngeneo.

Professor Helgen said Colin Groves was an original.

‘He was a gentle soul, but could be an immovable opponent. And he was genuinely brilliant, yet every bit as genuinely modest … When I think of Colin, I see him in my mind’s eye in his office at the ANU, decked from floor to ceiling with books and journals and reprints, all of his key resources, usually reckoned obscure to all others, within arm’s reach.’

This rings a cathedral of bells. Whenever something came up in our conversation about – well, almost anything – Colin would have a book, journal or anecdote to clarify, correct or corroborate any fact, no matter how obscure.

But my overriding memory of Colin isn’t his intellect or reputation, but his enormous kindness and placidness. He was never overtaken by anger, only bewilderment at the occasional fecklessness or waywardness of his fellow Homo sapiens.

He was one of my dearest friends, and his passing leaves a gaping hole in the lives of everyone who knew him.

Below is the eulogy I delivered at his funeral last Thursday.

Colin Peter Groves

As I look up at the Canberra’s first blue sky in five days, I’m tempted to think that while Colin did not believe in god, god almost certainly believed in Colin.

Although I knew him for 30 years it wasn’t nearly long enough, but perhaps long enough to discern the three great loves of his life.

Most importantly of all, his partner, best friend, constant companion and carer, Phyll.

Second, his love of science, particularly biology of course, and how it revealed to him the universe he shared with his fellow-primates, ungulates, big cats, avian dinosaurs, tardigrades, dogs, bats and cetaceans.

Third, his love of chinwagging. All the creatures I just mentioned could happily be included in a single lunchtime conversation with Colin. You might start discussing sexual dimorphism among species of African antelope and end by discussing the size of Donald Trump’s genitalia. (Amazingly, and somewhat distressingly, size does matter in nature.)

Let me deal briefly with each of these three great loves, from last to first.

It seemed to me that Colin was in his element when he shared conversation with friends and colleagues. If food and drink were included, so much the merrier, which added a cruel twist to the illness that eventually took him from us.

Although most discussions started with and usually revolved around science, his interests were catholic: skepticism, history, music, art, literature, film and television, and a hundred other subjects. He didn’t possess a ‘comfort zone’ as such; he was happy drifting on a sea of titbits, anecdotes, quotes, and bad puns (because, as Colin would patiently explain, a good pun isn’t a pun but a joke, and the quality of a pun is directly proportional to the volume of the groan it elicits).

He also had a deep and abiding love for startling and unexpected facts.

I remember how much he enjoyed discovering that the Great Pyramid of Khufu, built around 2560 BC, was the tallest building in the world until succeeded by – of all things – Lincoln Cathedral in 1311. A 3,800-year old record. He was just as delighted to learn that when Lincoln Cathedral’s centre spire collapsed in 1549, the Great Pyramid couldn’t resume its title as the world’s tallest building because erosion had reduced its height to below that of a church in Germany.

While an hour’s conversation with Colin could be filled with minor revelations such as these, they were never random thoughts. They were either staging posts that guided you safely to the end of a conversation, or points that illustrated a greater truth Colin was pursuing with the gentle doggedness of a modern-day Socrates.

In a conversation about intelligence and self-awareness, he might include the latest research about the Theory of Mind among corvids, Mozart’s Marriage of Figaro, gorillas studying their reflection in mirrors while trying on different hats, and the British television series Peaky Blinders. But every diversion would have a point, and every point would add weight in support of an argument for or against a main proposition.

I briefly mentioned Donald Trump. It seemed to me that while Colin never avoided discussing politics, what he cared about were the issues important to all of us in a free and democratic society, issues shaped and sometimes decided by politicians, pundits and lobbyists. It was people that Colin cared about, not cant. It was ideas Colin cared about, not ideology. What Colin wanted for our society was equality, opportunity, fairness and boundless curiosity.

Colin’s second great love was science, particularly anthropology and taxonomy. To say he was a biological anthropologist, while absolutely accurate, is entirely insufficient. Robert [Attenborough] has already talked about Colin’s amazing academic career, but I first met Colin because of his opposition to those forces that set themselves against science, particularly religious inerrancy, with a special focus on the shallow, silted stream of creationism.

From the first time I attended a meeting of the Canberra Skeptics, Colin immediately stood out as the most determined, the most knowledgeable and the most resilient opponent of creationism I have ever encountered. I never imagined someone as steeped in science as Colin would also be so utterly familiar with the Christian bible he could quote chapter and verse.

It wasn’t the idea of opposition that excited him, but the idea of investigating claims and when found wanting, standing up against them. I never once saw Colin angry, at least not in the sense most of us would understand the word, but when confronted by blind stupidity or blind faith, his eyes would open slightly in surprise, then narrow as he marshalled his arguments in defence of rationality.

The only other time I saw this response was when he was confronted by casual arrogance, wilful pride or careless prejudice. He understood how all these were used to stifle debate or to keep underdogs in their place, and he resented it.2

Colin was not a skeptic for the sake of it. It was just the flipside of the scientific method he applied to his everyday investigations of the natural world. It was as much a part of him as that sense of wonder that shone from him whenever he talked about the discovery of a new hominin fossil, or a new species of orangutan, or gravity waves.

Ultimately, forever and always, Colin’s greatest love was Phyll. On those few times I visited when Colin showed off just how much he knew about obscure science or history or culture, he wasn’t doing it to impress me. I think he was doing it because he just loved flirting with Phyll.

Phyll was his touchstone and keystone, his measure and the source of his strength. When she spoke, he listened. Even when he disagreed, he listened, and he listened closely.

And one never visited Colin, one always visited Colin and Phyll. They were as close to being a single unit as any two people I’ve ever met. Two minds, two voices, often two very different opinions, but a single soul, a word even Colin would agree with in this context.

They generously shared their life with family, friends, colleagues and students.

For that I will always be grateful.

[i] Mittermeier, Russell A. & Richardson, Matthew. Foreword to Extended Family: Long Lost Cousins, by Colin Groves. Conservation International, Arlington, 2008.

[ii] Helgen, Kristofer M. 2017. ‘Eulogy for Colin Peter Groves’, Canberra, 7 December.

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09 November 2017: the eighth great ape and the problem with ‘species’

Until recently, only seven species made up the group of primates known as the great apes, or Hominidae. Two orangutan species (Sumatran and Bornean), two gorilla species (eastern and western), two chimpanzee species (chimpanzees and bonobos), and us.

But in a report recently published in Current Biology, an international team of scientists announced a new hominid with fewer than 800 members, Pongo tapanuliensis, found just south of Lake Toba in Sumatra. To save your tongue twisting around that particular binomen, we can call it the Tapanuli orangutan.

The scientists compared skull, jaw and dental characteristics of a Tapanuli specimen with those of the Sumatran and Bornean species, and analysed 37 orangutan genomes as a second line of evidence.

Orangutan

Three species of orangutan: from left, Bornean, Sumatran, Tapanuli. Photo credits: Eric Kilby, Aiwok, Tim Laman

The report gained a great deal of media attention: not only because we humans had a new cousin, but because the Tapanuli is an endangered species.

However, there were dissenting voices. In an interview with the ABC, for example, Lee Christidis from Southern Cross University pointed out that the analysis had been carried out on only one specimen and that the DNA evidence was at best ambiguous.

It’s only fair to point out that it’s often the case that a species will be described by a single representative organism, or, as happens frequently in palaeontology, those fragments of a single organism that have been fossilised or otherwise survived over many millions of years.

The report also generated discussion about what we mean by the word ‘species’. Jerry Coyne, professor emeritus at the University of Chicago and author of the excellent Why Evolution is True, wrote in his blog:

‘Not only do I see this new “species” as merely an isolated and genetically differentiated population (as are many human populations regarded as H. sapiens), but I’d also contend that there is only one species of orangutan overall, with these three groups all being subspecies. Sadly, a lot of systematists don’t see it that way, as they seem to think that any isolated population, if it can be told apart morphologically or genetically from others, warrants being named as a new species. Yet to evolutionists, a “species” is not an arbitrary segment of nature’s continuum, but real entities that maintain their “realness” because they don’t exchange any (or many) genes with other such entities where they cohabit in nature.’

But is this indeed the definition of species with the greatest currency among most biologists?

To start with, there has to a definition that works across all fields. A primatologist cannot have a different concept of species from, say, an entomologist, or the whole point of taxonomy – the orderly classification of living things that demonstrates their evolutionary relationships – starts to fall apart.

This doesn’t mean that definitions in biology – or any scientific endeavour, for that matter – are written in stone. As our knowledge of the world around us grows, the language we use to explore, explicate and explain that knowledge must also grow.

The definition I was taught at school is not dissimilar to Coyne’s quoted above, and is based on what is called the Biological Species Concept (BSC), developed by Ernst Mayr and Theodosius Dobzhansky in the early 1960s (Coyne did some graduate work under Dobzhansky at Rockefeller University). As Colin Groves, professor emeritus at the Australian National University, wrote, ‘This concept states that under natural conditions a species ‘should not exchange genes with other species’[i]. Groves goes on to point out that ‘ … the popular idea that two species are “unable” to interbreed is  a misunderstanding: it is not that they cannot interbreed, it is that they do not.‘

The BSC was further refined by Mayr and Jared Diamond in a paper on Melanesian birds in 2001, and then in 2004 by the aforementioned Jerry Coyne with H. Allen Orr in a book about speciation called, appropriately enough, Speciation.

Groves argues that the modified definition of BSC risks different standards of comparison in different taxonomic groups: it’s a definition that won’t work across different fields, in other words.

Groves again: ‘If a genus contains a pair of sympatric[ii] sibling species (species that differ only slightly, inconspicuously), the standard for species recognition will be set much “lower” than in a genus in which sympatric species pairs are grossly different. It is the search for objective standards – for an operational means of distinguishing species – that has been responsible for the controversies that marked taxonomic discussions over the past 15 or 20 years.’[iii]Taxonomy

Many biologists now use what is called the Phylogenetic Species Concept (PSC), developed by American biologist Joel Cracraft from the early 1980s. Put very simply, in this concept a species is the smallest population of organisms that is measurably different from other populations sharing the same ancestry. Note that this concept says nothing whatsoever about species sharing genes, such as happened between Homo sapiens and H. neanderthalensis around 100,000 years ago.

It’s important to note that both the BSC and the PSC are attempts to operationalise the evolutionary concept of species; that is, that a species is an evolutionary lineage.

While the report in Current Biology describing the Tapanuli orangutan as a new species of great ape has, for the most part, been received positively, the fact that many distinguished scientists question the findings shows that the debate about what constitutes a species is ongoing.

[i] Groves, Colin. ‘Speciation in hominin evolution’; African Genesis: Perspectives on Hominin Evolution; ed Reynolds, Sally C. & Gallagher, Andrew; Cambridge University Press; Cambridge; 2012, p 46.

[ii] Sympatry occurs when two or more species live in the same geographic area.

[iii] Ibid.

07 October 2017: New evidence suggest we are much older than 300,000 years

In a recent blog I wrote about new dates for skulls found in the cave of Jebel Irhoud in Morocco in the 1960s. Originally assessed as belonging to Homo neanderthalensis (an assessment that was soon challenged), a reappraisal published in Nature this year confirmed they were in fact H. sapiens skulls; the great surprise was that the reappraisal determined them to be at least 300,000 years old.

Jebel Irhoud

Cast of Jebel Irhoud 1 from the Australian National University. Photo: Simon Brown

New work done by scientists in Sweden and South Africa, and reported in Science, have now dated DNA obtained from a 2000-year-old Khoe-San skeleton apparently unmixed with Bantu or Eurasian DNA, as having separated from other H. sapiens sometime between 260,000 and 350,000 years ago.

The San are the First People of South Africa, Botswana and Namibia. Indeed, they may be the First People, the ancestral group all modern humans are descended from, or at the very least very closely related to them.

The San are the most genetically diverse of all humans living today. In an episode of Catalyst on the ABC about her research on San DNA, Professor Vanessa Hayes said, ‘There’s more similarity between myself and a Han Chinese than between two San people.’

Bushman

San hunter/gatherer

As reported in Science, the recent work on San DNA involved several ancient individuals, but the standout dates were given by DNA from the genome of a hunter-gatherer boy known as Ballito Bay A. The scientists concluded that, ‘ … our results show that the deepest split among modern humans (the estimated latest time for the emergence of H. sapiens) occurred at between 350 kya and 260 kya.’

Given that the skulls found in Morocco have been dated to at least 300,000 years ago, it would seem not unreasonable to consider the older dates for the emergence of H. sapiens – 350,000 years ago – being closer to the mark than the lower date of 260,000 years ago.

This new evidence also adds weight to the theory that our species may have partly evolved in South Africa.

In the last eight months, we have seen conservative estimates for the age of our species jump from 190,000 years old to almost double that. It’s been an extraordinary year for palaeoanthropology.

22 May 2016: Crows got smarts

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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

global-mosaic-of-pluto-in-true-color

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.