Tuesday, 11 July 2017

Of open access, pay walls and sci-hub: a defence of the pay-wall perspective

OK – so my position is not that of a typical academic: I work from home, a remote location on the edge of a wilderness area, and I’ve never been able to make university library proxy mechanisms work for me. Instead, I’ve done what I’ve always done: email authors for pdfs, or in more recent years, google for on-line repositories. As a last resort, I’ll email our university librarian. Never in my life have I paid the $30 usually encountered with articles hosted by the big publishing houses. And yes, as of recently I am editor of a pay-wall journal.  

In the beginning, once upon a time, long long ago, I was pretty much a fan of the idea of open access: after all, it intrinsically appeals to the basic idea of what is right: that knowledge should be available to all. Later on, an open access journal then published an article stating that citation rates in open access journals were higher (shown later to be a controversial claim). In the meantime academics had 2 apparently good reasons to publish open access.

But we need to take a step back from moralizing self-righteousness: in the publishing world, there are people that need to be paid and so there are 2 revenue streams: either the author pays (open-access), or the reader pays (pay-wall).

So a couple of years ago I braved the submission system of Plos-One: the flag-ship of open access publishing. I was rather shocked towards the end of the submission to find out that there was a submission charge of $1500! That is right, one thousand five hundred US dollars. F me, that was more than my meagre research budget! To be fair, there was an application process to have this reduced (developing world submission etc etc), but after going through that there was still a fee of $200 liable upon acceptance. I was fretting about how to pay that for weeks, and I’ve never been so glad to get a reject-and-resubmit decision in my life. After revision, that article was subsequently accepted by a pay-wall publisher associated journal and I didn’t have to pay a cent.

Clearly, for the likes of non-university academics like myself, open access is just not a viable economic option. Ok – there are also very few non-university academics.

But that is not the end of it. For years now, almost daily somewhere in my spam box, occasionally filtering into my inbox, is a request from a ‘new’ open access journal of SCIENCE NATURE or NATURE SCIENCE or some combo of famous journal names begging for an article. Open access became a business model quickly adopted by a range of fringe science organisations, where profit clearly comes before quality.

And I’ll admit to having tested that out when an article that I’d written, not in my field of expertise and of dubious usefulness that had been rejected from reputable journal, was accepted pretty much as is for a fee of US$50. The journal was south-east Asia based, editors clearly struggled with English, and this was just one more article for their portfolio and a few more bucks in their pockets.  ‘Journals’ like that one thrive on the great pressure on researchers to publish-or-perish, and reach their minimum, surprisingly difficult to achieve, quota of 2 first authored papers a year.

The traditional news media world, e.g. newspapers, has been under pressure for some time now due to ‘free’ news available on the internet. However, with the rise of Fake News and click-bait leading us to advert filled web-pages, certainly many people are now willing to pay for quality and trusted content.  I suspect that pay-wall publishers are likely still around as they more or less are the guardians of good quality content. Certainly, there is a legitimate reason to request money to pay journalists and authors whose currency is words.  

The big science publishing houses of course have a portfolio of pay-wall as well as open-access journals. In a sneaky move by Wiley recently, a submission by a student I’m supervising to a good–ranking pay-wall journal was palmed off to a ‘sister’ open-access journal. When the crunch came to discuss payment, the journal wouldn’t budge on their fee: around R15 000. That is big money in conservation science. There was no choice but to withdraw and resubmit, to a pay-wall journal of course.

And now with the rise of Sci-Hub, where pretty much any article anywhere anytime is available through their super-efficient search and delivery system, all the world’s science is basically now open access.  So certainly, there is no longer the incentive to publish open access from the moral perspective of making your research available, except Sci-Hub is essentially peddling in stolen goods. Sci-Hub is certainly the Robin Hood of the publishing world at the moment.


I like that the logo for Sci-Hub is a bird (a crow?). In the spirit of Sci-Hub, I did not ask for permission to use this logo


While open access journals cry their amazing download statistics, lets face it: those of you who have accumulated vast pdf libraries, how many of those articles were downloaded with you thinking ‘I’ll read that later’ and you never did. Certainly, at a conservative estimate, I’ve never read more than the abstract of >50% of my pdf library. And abstracts are free anyway…

I’ll even go so far as to say that recently I’ve even felt angry with fellow South African’s who have published open access. Maybe they managed to get their fee reductions, but if not then not only are we exporting our science to foreign journals (a tirade for another day), but we’re paying for that privilege in a climate of #FeesMustFall! Certainly, there I must agree that the money set aside for academics to publish open access could be better used elsewhere (e.g. supporting the university libraries, student support etc).

So there we go: that is my voice against the ‘open access is better’ hymn I hear so often. Viva pay-wall publishing! If you can pay for your article, please do, and if you can’t: you know what to do.

Ps I was originally going to title this: “Does Sci-hub spell the end of the open access publishing model?”, but that is apparently not an original thought, should you care to google. But ironically, even sci-hub is not ‘free’ – there (illegal) operation is all run on donations, you’ll have to navigate their DONATE pop-up at some stage, and isn’t that really just a soft pay-wall after all?

Sunday, 11 June 2017

Of Gales, Cape Parrots and Crowned Eagle

Further surveys out of Grahamstown had to be cancelled due to gale force winds this week. Still, Wednesday morning Adrian Craig, Lynette Rudman (Eastern Cape Bird Club), Diane and myself headed out somewhat optimistically. Our destination was Fort Fordyce Nature Reserve, managed by Eastern Cape Parks and Tourism. This well signed, well looked after, quiet, forested reserve is quite a contrast to the Darlington Dam campsite.

We were warned on entrance that strong winds had already brought down two large trees, and we should park away from anything that might topple onto us. Ringing, our mission for the morning, was out of the question. Instead we went for some walk into the forest, where the trees did offer some shelter from the howling winds, but where birding was very quiet.

The birding highlight of the day would come late that afternoon on our way out. Lynette had some inside information that Cape Parrots were at the Baddaford farm stall. Sure enough, flutters of green and squeaks could be heard from the Pecan nut grove, and Lynette got us permission to head down a bit closer. The birding highlight for my day would have been the juvenile Crowned Eagle perched right overhead and that provided excellent viewing. But that would be eclipsed when eventually the parrots emerged en-masse from the green foliage. We’d been a bit disappointed when our trajectory to the pecan-nut grove had been cut off by an electric fence. As we stood wistfully wishing to get closer, trying to catch a glimpse of anything in the trees, suddenly the calling volume started to pick up. It was evident that there wasn’t just a small party of parrots here, but quite a few. However, none of us were prepared for the irruption of 160 parrots from the grove of trees that was no more than 100m long.

The parrots whirled and swarmed, many then settling in the large tree near us. The appearance of a Black Sparrowhawk caused further chaos to the clammering flock. Eventually, with the sun having disappeared from the valley, the flock took off and headed away, presumably in the direction of Hogsback, well know Cape Parrot hotspot.  Smaller groups were then observed coming down the valley, presumably from further off. The whole experience was stark contrast to my first efforts to spot Cape Parrot: I’d spent three days camping near Stutterheim just for a sighting of a pair flying high overhead. The Cape Parrots of Baddaford experience was a lot more reminiscent of the claylick experiences of the Tambopata River.

With the estimated population somewhere around 1500 birds, that we had seen roughly 200 (10 – 15% of the population), was a very very special experience.

Juvenile Crowned Eagle

Cape Parrots




Darlington Dam: Addo's best kept secret?



A dramatic week, with Cape Town battered by storms and the fires to the south of us wreaking havoc in Knysna: evacuations, houses burnt and lives lost in this historic seaside town. Despite that, the area is in the grips of a severe drought, with the sporadic rains from two months ago now a distant memory.

Still, my week started fairly well. I set off at 5am Monday morning to a Karoo Biogaps pentad just off the untarred R400 between Jansenville and Riebeek-east. The area was typical flat Karoo terrain, but with elements of succulent Albany thicket as evidenced by expansive stands of ‘noors’, a species of Euphorbia. The Sunday’s River, reduced to puddles, also winds its way through here. The pools of water and acacia thicket lining the river provided productive birding, with the cold early morning making way for a warm and pleasant day.

This was the first pentad where Sabota Lark would prove to be really common. Small parties were observed foraging here and there several times. White-fronted Bee-eaters provided some colour, and some nesting Rock Martins on the farmhouse were pointed out by the farmer. He also commented that he had seen Fish Eagle feeding on Angora lambs on infrequent occasions. The only raptor I’d see here would be the inevitable Pale Chanting Goshawk.

As I’d been unsure as to accessibility across the pentad, and the amount of time I’d need to survey it, I’d not made accommodation plans for that night. However, the farm tracks and dry conditions meant easy access across the pentad, facilitating timely completion of the survey come 5pm. I’d noticed the Darlington Dam was relatively nearby, and having never been there decided it would be a worthy place to explore for accommodation options.

I was somewhat (pleasantly) surprised to find that the dam falls under the jurisdiction of Addo Elephant National Park. However, unlike the main Addo section, things at Darlington are a lot more informal – there was no ranger at the gate, and I had to hunt around the houses to find someone who’d take money for entrance or camping. This proved to be very cheap – R60 excluding conservation fee, which must make it the cheapest SANPARKs camping fee of any of the national parks. I’d later find out that this is perhaps because there are no showers or running water: there is no ablution block along the lake edge to which I was directed. Toilets are very dilapidated and dirty long-drop toilets scattered along the lake edge. It is not surprising that there is toilet paper and poo behind most bushes, but the piles of litter were inexcusable as bins are provided. Darlington Dam is probably best known to the angling community, some of whom clearly need to clean up their act. Navigating catfish heads, shit and the litter along the lake edge is a putrid affair.

In fact, the original title for this blog post was Darlington Dam: Addo’s best kept (dirty) secret?

Enjoying the lake edge at the campsite was not what I was there for of course: the birding would make up for all that. Spotted Eagle Owl had already greeted me as I’d tried to navigate the un-signed tracks in the evening winter gloom to somewhere legal looking to put up my tent. Waterfowl and Water Dikkop bickering provided backdrop noise all night long. During the cold, long, pre-sunrise dawn was when I took my walk along the dam edge, where Red-billed and Cape Teal paddled off at my approach, Egyptian Geese and Shelducks complained loudly, and a variety of other birds provided distraction from the legacy of human presence. As a bonus, I was the only person there.

With the rising of the sun it seemed like a good time to go for a drive to explore the rest of the pentad outside the sturdy electric fence demarcating the camp area. For those more interested in game than birds, Jackal, Vervet Monkey, Baboon, Kudu, Gemsbok, Kudu, Rhebok or Reedbuk, Duiker, and Springbok were all seen. Meanwhile, birds of all sorts were non-stop along the water edge. I was surprised to see Cape Bulbul rather than Red-eyed Bulbul, and Karoo birds were generally lacking from the lengthy bird-list, despite the obvious suitability of the habitat. With 80 birds for the 4-5 hours birding, this is easily a site that could produce 100 birds for the day with a few more hours at this time of year, and probably a lot more with the summer migrants.

However, I had meetings in Grahamstown to get to, but on balance, I could have done with at least another day here. Addo clearly have big plans for the area, with a seemingly endless tract of sturdy electrified game fence stretching along the main dirt road. If elephant and lion aren’t there already, they will be soon.

Female Southern Black Korhaan

Blacksmith Lapwing

Familiar Chat on 'noors

Fish Eagle with a view

Grey-headed Gull


Kittlitz's Plover


Lark-like Bunting on noors

Red-billed Quelea, non-br

Sabota Lark

Water-Dikkop


Oh yes, despite this rather alarming warning sign, I did not see or hear hippo, or see any tracks. If that is because they simply avoid the human habited lake section I cannot say.



Friday, 26 May 2017

The SHE in my Machine

So I take it that since computers can now beat humans at Poker, Go, driving safely and pretty much anything else, that the Singularity has happened. Apart from a slightly embarrassed silence from humanity (after all, who wants to get on a chair and boast about how stupid we are), the world hasn’t changed much down the line of how sci-fi movies made out we’d all soon be slaves to machines.

After all, artificial intelligence is still useful, and cute, so long as we get to hold it in the palm of our hands. I mean, if our much-smarter-than-us-phones start to threaten us with slavery and nuclear war, we’d just flush them down the toilet and buy the next slightly less belligerent model. Clearly though, if the machines are seeking dominance over us mortals, something that hasn’t been solved by them is the disconnect between computer reason and the human need to go where no man (or machine) has ever gone before. Let’s take the example of surveying birds in the Karoo.

The Karoo: dry, big, open space, endless dusty roads, a winter landscape drawn solely from the brown end of the colour spectrum, and where what counts as excitement here is watching a sheep getting so bored that it falls over asleep. And there are snakes: poisonous ones. I suspect that somewhere in the Karoo they’ve buried a black hole, because time warps here like nowhere else: a 20km drive can feel like eternity. Our computer is thinking: why do you even want to be there? Why would you go from one point in this landscape where everything looks the same, to somewhere else that looks like the place before?

Computer diagnosis: you are mad and I’m going to quietly steer you to a psychiatrist who will hopefully sell me to a homeless person on gumtree.com.

So how did I figure that out? Well – I got lost on the first survey based out of Richmond: purely my own fault, based on too little sleep and not figuring out one dirt road from another. Seriously though: intersections on the back roads are rarely marked, and if they are it will be something like “AP1056” or “Turn left in the direction of a-town-you’ve-never-heard-of that sounds like a planet from Star Wars”. Alternatively you might want to go right.

That evening, surveying co-team lead Gigi Laidler showed me a neat trick: I could just enter the GPS coordinates of where I needed to go straight into Google Maps on my phone.  I.e. from ‘Your location’ aka in machine speak ‘Why are you even here? There is nothing here! You’re clearly lost’ to ’32.123s 23.145e’ aka machine speak for ‘Why do you even want to go there? Clearly there has been some mistake!

Never-the-less, a cute little blue line wiggles its way across the Google map. What is not so evident is that artificial intelligence is manifest in the Navigator: i.e. that seductive voice that tells us that in 600m we should be turning right. (Personal confession, I never thought that ‘In 600m, turn right’ would ever send me instantly into daydreaming about Scarlett Johansson, although in retrospect clearly this is part of the machine’s plan to control me because inappropriate daydreaming will definitely get me lost and hence I become more reliant on Google Maps for finding my way, ie. a downward spiral of addiction).  

Thanks to Google for that photo collage of the famous actress: apologies to any photographers not credited


The first attempt worked quite well: we were headed for a survey block just off the N1. Scarlett Johansson was clearly thinking “Yes! let’s get there, at least its 50km closer to Cape Town!”

The next journey would reveal the truth about the artificial intelligence in my machine. I entered coordinates for a pentad to the north, literally in the middle of nowhere. Up popped the little map, which I perused to see if it made sense, and it did. I confidently pressed the navigator button, and let Scarlett Johansson tell me I needed to turn right at the first intersection – one satisfied humanoid at the wheel!

A few kilometres down the road towards Richmond and Scarlett was having a panic attack: the screen had frozen. Clearly Scarlett was torn between needing to act in self-preservation and the need to obey her mad human master, although I’d only realise that later.

Since I knew this bit of the road, I closed the app while I navigated to the other side of the town, where I started the app again. I waited for Scarlett’s sultry tones, but she was speechless with fear. The first intersection loomed out of the pre-dawn gloom unannounced, but I was confident I needed to turn right (somewhat disappointed that I needed to have to do that alone).

A few kilometres further down the road and I shot by another un-named intersection. Didn’t I have to turn right here? I braked to a sudden halt. While I was trying to interpret blue dots from blue lines on the map Scarlett suddenly commanded: “Continue straight”.
“Are you sure Scarlett?” She remained silent, and I forgave her: I mean, she’s good looking and we all know a GPS can get confused from time to time; after all, I was very close to the intersection. Correcting myself onto the right road, I continued on. As the red-glow of dawn started to show off the table-top mesas, I glimpsed another intersection up ahead, helpfully named “AP random number”.
Continue straight!” commanded Scarlett. Reasoning that the command had been given with sufficient time and that she’d settled down, I continued straight, beguiled by the outlines of the curvaceous landscape.

But it dawned on me as dawn broke, that according to my odometer I should be where I needed to be, and that Hannover was not where I wanted to be heading. I looked down at the map, and was horrified to see that the blue dot of my position was now about 15 km from the blue line of the Google map! Clearly it was time to shut down Scarlett and resort to manual navigation.
Don’t take me to that land of no internet or cellphone reception! Don’t disconnect me from the Cloud! NOOooooo…!” silently wailed the virtual Scarlett.

Yeah right, like you’re gonna Ex Machina my ass – I’ ve got birding to do…. And that’s is what will always make us better than the machines: our bizarre desire to go odd places to take photos of little brown animals in a desire to better understand and protect them. It’s not logical, and hence Scarlett and I will never have much in common.


A Desert Cisticola on a precarious perch

Shocking picture of a Jackal Buzzard!

A poplar tree in late autumn colours added some color to the scenery


In my last post, I was pondering the lack of Lark-like Buntings. This time it was hard to do a point count without recording Lark-like Buntings: they were everywhere. Clearly the summer rains had done their job in the north-eastern Karoo region, and birds were loving the grass and seed cover. Pentad lists were between 50 and 70: double those of last months.


However, since its been some time since the last good rains, birds were regular visitors to water wherever it occurred: here a Lark-like Bunting takes a drink from a puddle next to a livestock watering trough.

Northern Black Korhaan - these noisy birds have been known to throw rider's from there horses when irrupting from cover at the last minute.

Namaqua Warbler in full cry


Plain-backed Pipit (YES IT IS!)

Rufous-eared Warbler

The lack of color the rest of the day makes sunsets especially pretty


During the heat of the day during one survey I waited by a small stream to watch the birds drinking and bathing. Red-eyed bulbuls were most frequently observed.

Puncture! Scarlett made me drive over that screw, I know it.



At one of the survey sites the farmer's dog decided to take me for a walk. Here 'Otto' surveys his kingdom.

While intersections on Karoo roads are poorly marked, bizarrely enough beautiful sunrises are well signposted.


Interesting ornithological observation: a group of non-breeding Southern Masked Weavers and Red-headed Finches were observed eating harvester termites at one point.



 


   




Monday, 15 May 2017

Break to Borneo

Its 6pm, the end of my first full day in the city of Bontang, East Kalimantan, Indonesia. The cicadas are battling to be heard over the mosque loudspeakers issuing the evening call-to-prayer. I'm on the edge of an 18-hole golf course fringed by mangroves. Looking beyond the mangroves is a wooden village on stilts in the water. Everything feels kind of surreal: it took 4 flights with over 17 hours flight time and a 6 hour taxi ride straight out of gran-turismo to get here, more than 36 hours travel time.

You know you're headed somewhere remote when the bookshops in the airports don't have a travel guide to where you are going. In transit through Singapore I found the first travel guide to Indonesia, as thick as my middle finger, and it had 2 pages on East Kalimantan on the island of Borneo. In Jakarta, I find one Lonely Planet guide to Indonesia: I buy that and a bird book. I'm the only muzungo / gringo on the plane for the last flight to Balikpapan.

So: Some fast facts about Indonesia: it is an archipelago of over 17 000 islands, the largest of which
are Sumatra, Java, Borneo, Sulawesi and Papua. Indonesia is the world's 4th most populous country with over 255 million people. The official language is Indonesian, although that is a second language to 80% of the population. Even at the pretty fancy 3 * hotel, the English of the staff is basic at best, although that is not a bad thing: watching the waitress do an impression of a cow to explain an item on the menu will go down as a highlight of the trip.

I was last in Borneo more than 20 years ago as a backpacker, and then only on the northern Malaysian side: Sabah and Sarawak. However, most of the island belongs to Indonesia.

The reason for my visit to this area is not for birding! It is to learn about an IUCN project that uses species traits to examine their vulnerability to climate change. But more about that later. The first few days when not on the laptop I've been out birding in this tropical environment as much as possible.

Birding Bontang, Borneo.

While some countries, like Peru, have bigger total species lists, Indonesia has the highest number of country specific endemics: 381 of 1605 (24%) species! Perhaps as to be expected with such huge human impact, about 20% are considered to be species of conservation concern according to Morten Strange's Birds of Indonesia (the only bird guide to the birds of the entire archipelago, but even so only with 912 of the total number of species).

Some important Borneo birding facts: there 52 endemic species of the 669 species that can be seen here. The best bird book is Phillips' field guide to the Bird of Borneo. An example is one of the quick id by habitat plates, which pretty much was a one stop id page for birding around the hotel.

I'd only find out later that there was a sign saying 'entry forbidden' – it was in Indonesian, so I spent several afternoons and a bit of a morning out trying to spot feathered creatures in the secondary forest and mangroves lining the golf course.

One day of the workshop included a day trip into the Kutai National Park. This park was declared by the Dutch in the 1930's and has been shrinking ever since: originally 3 million hectares, it is now less than 200 000ha. That is admittedly still pretty big, but the drive along the road that skirts the edge of the park revealed massive rural settlements and oil-palm plantations in the park. With open-cast coal mines to the north, and oil palm plantations to the south, the protected area is under massive pressure. Droughts associated with El Nino meant that almost the entire park burnt sometime in the 90s. Given all that it is practically a miracle that Orangutans are still found here. An estimated population of between 1500 – 2000 is found in the park. It is one of the best places to see wild Orangutan in Indonesia, although certainly also one of the least straightforward to access, unless you come with your own car and a lot of preparatory work.

As promised though, after a couple of warm up walks through the forest, and a typically amazing Indonesia buffet that included things like Snake fruit, battered shrimps, we were rewarded with views of the arm of a large male Orangutan reaching for figs in a tree on the side of the river. Later, after another walk we had spectacular views of a female feeding very close to the staff accommodation of the rest camp / ranger post. Our group of researchers weren't the only ones to get great views, a local news documentary crew were also on-site.

Although a bit late in the day for birding, certainly the highlight of the walk through the forest with local guide Harya was the Greater Slaty Woodpecker, a Bornean endemic and also the largest woodpecker in the world! The photos are more personal glory shots than images that capture the beauty of the bird.

So what was the workshop all about? Anne Russon does research on Orangutans from the perspective of the development of intelligence. Of course she is also very concerned about them on an individual level, since these magnificent red-haired cousins of ours continue to be poached, with youngsters sold for the pet trade. The large number of rehabilitation and reintroduction projects across Borneo attest to conservation efforts aiming to deal with this. However, the threat of deforestation and fires (predicted to increase under some climate change scenarios) is a real concern, and so Jamie Carr, Climate Change Programme Officer of the IUCN Global Species Programme had organised this workshop to do a life history trait based assessment to climate change vulnerability. What is going to come of that.... you'll have to wait and find out!

In the meantime, enjoy some of the scenes from Borneo, and visit the forest while you can, as it is disappearing incredibly fast, as are the animals that rely upon it.













These photos in high res plus More photos:




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