Nature

15 September 2018: The not-so-big (but still mightily impressive) ten

Last weekend, AJ and I went camping at Pilanesberg National Park. Well, I say camping. Our tent had a refrigerator in it. And a kettle. And power points for our mobile phones.

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Extraordinarily rough camping conditions prevailed at Pilanesberg.

Anyway, together with some fellow teachers from AJ’s school we went comfortably camping at a park famous for providing visitors the opportunity to catch sight of the Big Five: Cape buffalo, elephants, leopards, lions and rhinos.

While we did manage to see a line of lying lions in the distance – we needed binoculars to find them – for the most part the Big Five managed to elude us.

This is probably because AJ and I decided to forgo the chance of getting up before sunrise and braving subzero temperatures to tour the park in an open truck. Those who did make the effort not only managed to see the Big Five but cheetahs as well. However, they were cold. Very cold. Their fingers snapped off trying to focus their Nikon 70-300 zoom lenses.

We, on the other hand, got up at a civil hour, had a hot breakfast, and entered the park about 9.30 am, courtesy of the generous school librarian and his huge red ute. Although most of the predators and large herbivores had by then decided to migrate to warmer climes, we did see plenty of impressive wildlife, including kudus, wildebeest, zebras and giraffes.

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Grey heron.

And our fingers didn’t drop off focusing our zoom lens. Not just because it was warmer, but because our camera decided to stop working, forcing us to rely on the cameras on our mobile phones.

In fact, we didn’t really have to leave our tent to see some very impressive locals. Our camping site had been colonised by a several groups of impala, vervet monkeys, chacma baboons, banded mongooses, hornbills and helmeted guinea fowls.

The impala were the most impressive of all. They’re magnificently streamlined antelopes with a colour scheme designed by an Italian fashion house. The males sport magnificent horns shaped like ancient Greek lyres. The effect is somewhat spoiled when the males start practicing for the rutting season by pretending to come to blows and blowing through their noses, sounding like a parcel of agitated pigs with head colds.

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Impala cleaning his nose in preparation for a good snort.

The funniest sight is watching the normally docile guinea fowls suddenly scatter, running one way and then the other. AJ said the bird reminded her of a fusty old women from the 19th century picking up her skirts and pelting down the street.

The vervets spend most of their time high in trees or sitting like sandstone statues on the roof line of the campsite’s restaurant. They look down on their fellow primates with aloof disinterest.

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Vervet practising aloofness.

One of the highlights of the expedition was totally unexpected. We came across the ruins of an iron age kraal not far from the park’s entrance. The area’s fenced off, and if the main gate’s red light is flashing – meaning something like a lion or leopard or elephant is also touring the ruins – you’re advised to stay out. On this occasion we were the only visitors.

The kraal was built by the Tswana chief Pilane, hence the name of the park. The ruins are well signed, giving a brief history of the kraal and what the various buildings and spaces were used for. The kraal’s main lookout provided wonderful views of the park. It reminded AJ and me of some of the ancient hill forts on the border of Wales and England we visited in 2010. Although those hill forts weren’t surrounded by thorn trees. I managed to get one long branch wrapped around my left leg. It took some doing to disentangle myself, and the small wounds made by the thorns itched for hours afterwards.

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Warning outside the iron age kraal.

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The kraal itself!

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View from the kraal lookout.

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Thornbush.

A second highlight was the visitor’s centre, where people can eat and drink on a wide deck overlooking the bush. A large salt lick is placed not far from the deck, drawing giraffes, zebra and wildebeest, although when we were there only one giraffe, the biggest, got to enjoy the lick. He’d tolerate other giraffes having a go, but didn’t hesitate kicking any wildebeest who came for their turn. The zebras were pluckier than the wildebeest, but no more successful.

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A giraffe. Not a zebra or wildebeest.

The landscape between Johannesburg and Pilanesberg is eerily familiar. Geographically and botanically it’s very similar to the Southern Tablelands, especially the stretch between Canberra and Yass. It’s not surprising, I suppose: South Africa and Australia were once joined at the hip. The soft landscape is covered in grasses and acacias and other plants adapted to a hot, dry climate. True, South Africa has lions while Australia has sheep, and South African kopjes are rockier than Australian hills, but nonetheless …

The similarity even extends to bushfires. Pilanesberg hosted its own bushfire the week before we arrived, and large parts of the park were black and ash grey, again strangely familiar to anyone from inland New South Wales.

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Bushfire damage.

It’s not like AJ and I are looking for similarities, but perhaps a little homesickness makes you look for them instead of the differences.

In October, we hope to make our way southeast to Durban for a few days, stopping over at the Drakensberg on the way.

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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.

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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.

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.

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.