Friday, November 29, 2013

Botany picture #123: Bauera rubioides

Bauera rubioides (Cunoniaceae), Tasmana, 2013. This species appears to be extremely widespread and common across Tasmania but we saw it most frequently on the more heathy margins of rainforest areas where it would form large tangles. The flowers are all hanging downwards, making me wonder who the native pollinators are. Whatever the case may be, I assume that the introduced bumble bees will not have any problem with them.

Thursday, November 28, 2013

Inflation in citation metrics

On Jeffrey Beall's Scholarly Open Access blog I recently got involved in a short discussion on steadily rising citation metrics. He discussed a citation metric that he considers suspicious, and one of the reasons he mentioned was that it always seems to be going up. It is well possible that the metric in question is manipulated - or not, I would not know and have no opinion either way - but it is important to realize that some degree of inflation is unsurprising and not necessarily, on its own, an indication that something is off.

The most highly regarded of them all, the Impact Factors (subsequently IF) from Thompson Reuters' Journal Citation Report, show the same trend. Yes, there are some losers and a lot of stagnation especially at the lower end of the spectrum, probably because the editor of a very small journal is only willing to invest so much time into it, and if you only compare across two years or so you will get a lot of noise. But if you take a bunch of decent, mid to high level journals from my field and compare their current IFs with what they had a few years back you will see slight increases very nearly across the board.

Here a few semi-randomly chosen journals from my field and their change over five years - meaning I looked up the IF 2007 and 2012 for a few well-regarded journals whose names immediately popped into my head:

Am. J. Bot. +0.074; Aust. J. Bot. +0.217; Aust. Syst. Bot. +0.488; Bot. J. Linn. Soc. +1.514; Flora +0.559; Folia Geobot. +0.432; Syst. Bot. -0.345; Taxon +0.258; Trends Plant Sci. +2.813

The only one bucking the trend here is Systematic Botany, which does seem to have moved from publishing a lot of phylogenies to a lot of alpha taxonomy lately, and the latter unfortunately and unjustly does not bring in a lot of citations. Conversely, the Botanical Journal went up a lot since they stopped accepting purely alpha taxonomic papers and they published the last Angiosperm Phylogeny Group update, a landmark paper that was guaranteed to get a ton of citations. Trends also looks like it got a big increase but it is not that much relatively speaking; as a review journal it was always by far the highest on this short list.

So how is that possible? Why do the citation metrics appear to consistently increase over the years? Is there some manipulation going on?

Wednesday, November 27, 2013

Botany picture #122: Ozothamnus reflexifolius

Unsurprisingly I now have a number of plant photographs from Tasmania that I am going to use for botany picture posts in the next few weeks. We start with Ozothamnus reflexifolius (Asteraceae), a shrubby daisy that is known from only one population on a hill flank near Hobart. I has only been described as a new species a few years ago. Being so rare and vulnerable, it is good that the Royal Tasmanian Botanic Gardens have it in cultivation, and that is where I took this picture. I was extremely happy that I was able to see this plant during my visit.

Tuesday, November 26, 2013

When should we admit that somebody is perhaps a bit stupid?

Going through the newspapers that have accumulated while we were away, I came across this little piece in the Guardian on women supposedly going off contraception because it is too bothersome. The commenters on the online version have raised issues with argumentation from anecdote but that is not what immediately occurred to me.

Saturday, November 23, 2013

Tasmania, part 5: back in Hobart

Vacation is over. For the last few days we came back to Hobart and explored the area around it a bit more. The following is then not about landscape but about tourist attractions.

One day we spent at Margate. The Inverawe Native Gardens pictured above are not really a botanical garden in the strictest sense but a landscape garden run by a retired couple. Because it was raining all day, they looked somewhat surprised that they had any visitors at all.

As the name indicates, the garden has a focus on Australian native plants but in addition there is much information on early explorers of the area and on the earliest botanists. There are also timber samples, poems on nature and gardening to be read, and various whimsical pottery sculputures ranging from elves across the snails depicted above to weird hands sticking out of the ground.

Something for everyone I guess. We were of course mostly interested in the plants. The above are the beautifully spotted flowers of a Prostanthera (native mintbush, Lamiaceae).

Directly next to the gardens is the Margate Train, an old decommissioned train that has been turned into a range of shops: a bookstore, a speciality food store, a barber, an antique book shop, a gift shop, and a great pancake restaurant.

On a day with much nicer weather, we visited the model village of Old Hobart Town in Richmond. This is a miniature of Hobart as it was around 1820, with lots of informative signage on history and the changes that have occurred since that time. The plan one is given and photographs on the signs allow a direct comparison of the model with Hobart as we experience it today, for example where a body of water has now been filled in etc. The small clay figures of settlers, soldiers and convicts are very amusing, with some of them shown in engaging or funny situations, for example drunk, making out on a haystack, or stepping into a paint bucket. For the plant enthusiast, all the trees in the model village are live bonsai Nothofagus (southern beeches). All in all well worth a visit.

Finally, today we explored the famous Salamanca Market in Hobart, again bracing rain. Even found a few useful things. Tomorrow it will be back to Canberra.

Wednesday, November 20, 2013

Tasmania, part 4: Western Wilderness

Western Tasmania is known for its vast expanses of untouched, impenetrable wet forest. We were also delighted by the nice mountain peaks all around us. The picture above, taken at a lookout between Derwent Bridge and Queenstown, can perhaps give a bit of an impression.

We were staying in Queenstown, which had the advantage of being nicely central with easy access to the national parks to its east and the coast to its west. Unfortunately from an aesthetic perspective, it has long been a centre of the Tasmanian mining industry. The above picture shows a part of the famed Western Wilderness of the island after open cut mining.

The information signs around town must have been sponsored by the mining industry because they oscillate between (a) outright pride at how the area around Queenstown looks now and (b) acknowledging the devastation but attempting to shame the reader into complicity. The one above this mine, for example, pointed out the following, and quite correctly it has to be admitted:
We mine the copper but you use it! You might not realise, looking out on this mining landscape, that this is all about you. Copper is still mined at Queenstown and it is a critical part of what keeps our cars, houses, computers and mobile phones working.
So hey, maybe we should buy less shiny new electronic gadgets and recycle more metal? Yes, we are collectively sawing off the branch on which we are sitting; nobody can escape their partial responsibility. Still, some of us cheer for waste and destruction but others at least try to slow the process.

Case in point: The Franklin River, focus of one of Tasmania's great politial battles of the 1980ies, when those who wanted to dam it for electricity generation clashed with those who wanted to keep this last natural river system of the island intact. Whatever you may think about it - and water power is clean energy, no doubt about that - the latter side won, and now the river brings in money as a tourist attraction.

This beautiful waterfall is Nelson Falls at the western end of the Franklin Gordon Wild Rivers National Park. Both here and at other nature walks in the area you will find several information signs on the flora and the geological history of the area. I just wish they would have consulted a knowledgable botanist when they wrote some of them...

Telopea truncata (Proteaceae), the Tasmanian Waratah, at Scarlet Creek. I have now seen three of the five species of the genus, hooray!

A beautiful moss at Hogarth Falls Nature Walk. These rainforests in western Tasmania must be paradise for bryologists. Unfortunately, I do not know the name of this intricately branched species.

Sunday, November 17, 2013

Tasmania, part 3: the east coast

After the Tasman Peninsula, we went on to the east coast of Tasmania. We spent three nights at Swansea. Although the local Bark Mill Restaurant is as great as its fame would have it, and although we were happy with our accommodation, next time I would probably stay in neighboring Bicheno. The town is more scenic than Swansea, and at least at this time of the year the beach was much cleaner.

The blow hole at Bicheno. As my wife noted, all blow holes she had seen before including one on this trip at the coast of the Tasman Peninsula "worked" only when there was exceptionally stormy weather. This one appears to shoot water up all the time, even under average weather conditions. And the rocky coast around it was great too - massive boulders covered by weirdly coloured lichens, water pools, kelp forests, definitely worth a visit.

The other full day we went down to Freycinet National Park. This picture shows Wineglass Bay seen from the eponymous lookout. Beautiful but admittedly not particularly interesting botanically, at least not for me.

Another scenic spot in Freycinet, the Tourville Lighthouse.

Remember the weird grassy sculptures in the Royal Tasmanian Botanic Garden I wrote about a few days ago? Here is the real thing: a Xanthorrhoea, or grass tree, directly north of Freycinet. They often flower after fire but this one probably just thought now would be a nice time. The botanic garden where I studied in Germany had two grass trees. When they flowered once every few years that was a newspaper-worthy event, and some people would visit the garden specificaly to admire these exotic plants. And here we are and they are just another plant on the roadside...

Another thing that struck us recently was that certain areas of Tasmania were very much dominated by some species of introduced weed, and that the weed in question varies strongly from one region to the next. When we drove through the Midlands a few days ago, everything was full of some broom (we did not undertake to figure out what species). In some parts the locals tried to unroot and burn them, in others they appeared to have given up. On the east coast, on the other hand, we saw enormous stands of Centranthus ruber (Valerianaceae, shown above). And yes, ruber, that is another thing. As indicated by that name, the species is usually red-flowered but most plants here are white, as the one in the picture.

After the east coast, we made our way west, staying one night at Bronte Park Village which I remember fondly as being our base for the Skullbone Plains Bush Blitz about 18 months ago, when I first visited Tasmania. We were proudly informed that the Village would accommodate another central plateau themed Bush Blitz in the near future. Good for them!

Tuesday, November 12, 2013

Tasmania, part 2: Tasman Peninsula

We spent yesterday and today exploring the Tasman Peninsula. Yesterday we started by spending some time near Eaglehawk Neck, at a place called Tessellated Pavement.

It is known for the strange rock formations at the coast. As can be seen in the above photograph, they look oddly rectangular, as if they were man-made, but their shape is due to a natural though rare form of erosion.

This is a botany blog, so here is a plant: Plantago triantha (Plantaginaceae) growing on the rocks at Tessellated Pavement. By the way, when I need to identify Tasmanian plants, I use a fantastic online recource provided by staff from the University of Tasmania. It is a fairly standard usually dichotomous analytic key but it contains lots of images and buttons that can be clicked to obtain further information, making it much more versatile than a printed flora. Also, the characters used are generally very straightforward, with a focus on what can easily be ascertained even by a non-scientist. If you ever need to find out the names of Tasmanian plants, give it a try!

And this is the view from the Eaglehawk Neck Lookout at the turnoff to Tessellated Pavement. Apart from the above "pavement", this beautiful coast shows many other interesting shapes of erosion...

...such as arches. This is the Tasman Arch a bit to the south of Eaglehawk Neck. Look at the size of the Eucalyptus trees on top of the arch - this thing is massive.

Today we had less luck with the weather than yesterday, so it was perhaps good that we spent less time outside. We visited the ruins and museum of the former convict colony at Port Arthur, pictured above.

In a way, it is really quite a depressing place. Although at the time seen as a major advance because it gave criminals a chance at rehabilitation through useful labour and perhaps an education (as opposed to simply hanging them), it loses some goodwill once you read about the conditions under which the convicts had to live. With dangerous work conditions (mostly tree felling and mining), insufficient nutrition given the hard physical work, and apparently often cold and moist accommodation, one could also make the case that many of them were simply worked to death, often dying from accidents or respiratory diseases like pneuomonia. And that is before one realizes that some of the convicts were transported to the colony for ridiculously small offenses. The separate prison where all inmates were kept in solitary confinement as a matter of routine practice was basically just one massive, sadistic, psycho-torture chamber.

Port Arthur was also the site of the worst mass murder in recent Australian history, an event that prompted the country to enact stricter gun laws. It is interesting to note that the Tasmanians have also enacted a form of damnatio memoriae: as far as I can see so far, museums, travel guides and memorials all carefully avoid mentioning the name of the murderer.

Finally, at the end of the day we visited Remarkable Cave. (The Tasmanians have some of the most matter-of-fact place names in the country, although for me nothing beats Useless Loop in Western Australia.) What is so remarkable about it is that it supposedly resembles the shape of Tasmania. We could not quite figure out from what angle that is supposed to work best, so judge for yourself.

Sunday, November 10, 2013

Tasmania, part 1: Hobart

In our first two days in Tasmania, we have taken a stroll through the centre and harbour of Hobart, visited the Tasmanian Museum and Art Gallery, went up to the top of Mount Wellington, and visited the Royal Tasmanian Botanic Gardens.

View from Mount Wellington. This is also the first time since 2010 that my daughter has seen snow, and of course then she was less than a year old so she does not remember it. The weather was not optimal today but clear enough to have a good view.

The 'conservatory' glasshouse of the Botanic Gardens.

The lily pond of the Botanic Gardens.

This was weird. In an area labelled 'eucalyptus woodland' there were several of these sculptures consisting of soil and grass. There is a limited number of possibilities what they might be supposed to be. It could be that they are supposed to fool the visitors of the garden into thinking that they are grass trees (Xanthorrhoea), perhaps because the real thing does not survive in this climate(?). It could be that while the designers are well aware that nobody would be so stupid to mistake these as real grass trees, they are supposed to symbolize grass trees in this woodland habitat. Or they could be supposed to be art... somehow. I don't claim to understand the workings of the artistic mind.

Whatever their purpose, they remind me of that zoo in Gaza that painted stripes on donkeys because they could not get real zebras.

Thursday, November 7, 2013

Not much this week but watch this space

I cannot blog a lot at the moment because it is an extremely stressful week, and it is an extremely stressful week because it is the last before our family holiday in Van Diemen's Land. Stuff needs to be done before that. On the plus side, this means that I will hopefully be posting a few nice plant and landscape photos here from time to time, internet access permitting. Yay!


In science spam news, my junk mail folder currently contains a "call for research articles" from the "Global Advanced Research Journal of Food Science And Technology (GARJFST)". Yes, that is the name of the journal, no joke.

Botany picture #121: Leptorhynchos squamatus

This cute little daisy is one of my favorites here in the area. Leptorhynchos squamatus (Asteraceae), commonly known as 'scaly buttons', Australian Capital Territory, 2013.

Tuesday, November 5, 2013

Botany picture #120: Asperula conferta

Sometimes I am surprised that a plant that I first thought to be obviously a weed turns out to be native. This is an example: Asperula conferta (Rubiaceae), New South Wales, 2013. Looks just like the Galium and Asperula in Europe, so I wrongly assumed it had been introduced from there.

Monday, November 4, 2013

Dirk Gently's Holistic Detective Agency

Among the other books that I picked up at the recent book fair are both Dirk Gently novels. At the beginning of the year, I reread Douglas Adam's Hitchhiker novels and found that they were not as good as I remembered them. Compared to that, his Gently novels have two advantages: I had not previously read them, and somebody told me that they would be better. I have now read the first one, Dirk Gently's Holistic Detective Agency, and am indeed pleasantly surprised.

Spoilers ahead.

Friday, November 1, 2013

Distribution modelling, or: muwahaha, vindication!

Distribution modelling is an increasingly important technique in which one tries to infer where a species occurs, or at least can occur. The principle is at the same time mathematically complex and conceptually simple:

You take a number of variables that might influence whether a species can occur in an area or not - this could be lots of different things such as average annual rainfall, average temperature, average temperature in hottest month, minimum temperature, phosphate content of the soil, pH value of the soil, etc. Then you need geocoded known occurrences of the species you are interested in, the more the better, and in some models also known absences, and a fancy piece of software can produce the distribution model for you, projecting onto a map the likelihood with which the species will be found in each of the map's grid cells.

Potential uses of distribution modelling are many. You could be interested in how far a newly arrived invasive organism is potentially going to spread in your country, so you model its potential distribution based on data showing where it can survive in its area of origin. You might be interested in where a species can live and where it cannot live in the year 2100 given this or that climate change scenario. Going back in time, you might want to know where a species was able to live during the last ice age. If you can reconstruct the probable niche of ancestral species, you might also want to know where they would have been able to live given paleoclimatic assumptions.

In a paper published last year, I and a few colleagues made another use of distribution modelling. I was interested in the distribution of species richness of daisies across the continent. The problem is, inferring the species richness of grid cells from known occurrences will often be an under-estimate of the real species numbers because some areas are vastly under-sampled. In extreme cases, you may infer a species poor area to be as rich as a hotspot of diversity if the former is very intensively sampled and the latter is rarely visited by field biologists.

So what we did was to construct distribution models of all species of my study group and then stack them on top of each other to see how many species would be in each grid cell. As mentioned above, what you get is a probability of occurrence. How do you add them up? We did it quite directly: If a cell had, hypothetically, ten species with probability of occurrence of 50% each, we would have added that up to five species.

Some reviewers did not like the idea at first and argued that we should use some cut-off: Set all species that have more than X% probability of occurrence to present, all others to absent, and then count the presences. In the end, however, we convinced the editor that our approach made more sense.

And guess what? Last week I found a paper presenting a meta-analysis on the issue because they cited our study. Calabrese et al. examined ours and numerous similar studies that used stacked distribution models to infer species numbers, and they concluded that what we did was exactly how it should be done! The cut-off approaches used in many other papers vastly over-estimate the real numbers of species.

Feels good. As a colleague said, "it is nice to get feedback in a citation!" And next time I do something like this, I will have a reference to justify why I am doing it that way.