Saturday, May 31, 2014

Europe day 11: Chateau de Peyrepertuse

Another big tour today. We visited the Chateau de Peyrepertuse and the Gorges de Galamus, both among the most popular tourist destinations of the area.

The chateau is one of the most spectacular Cathar fortifications, and it costs EUR 6.50 per adult to visit. This is the upper castle of Peyrepertuse as seen from the lower castle. Even getting to the lower level is already a tiresome climb; getting up there even more so.

But it is so worth it - here is the view of the lower castle from the upper one. Note the many corners of the structure. The builders had to construct it into the rock, making use of whatever space they could find. I wondered in what was labelled the governor's room why there was so much rock on its floor that nobody had chiselled away, and whether the apartment had two maisonette-style levels of wooden floor when the castle was in use.

The second locality we visited were the Gorges de Galamus. If you look closely you can see the is a hermitage built onto the shoulder of the mountain in the middle of the picture. There is a path to the hermitage but we decided we did not have the time to visit it.

And this is the gorge itself. The tiny figures on the right are my wife and daughter, to demonstrate just how deep and steep the valley is. Unfortunately, a French society of vintage car enthusiasts decided to have their annual meeting in the area, and when we had to pass through the gorge their convoy of dozens of cars came the other way. Which is not something that the gorge can easily accommodate.

(Interesting, by the way, that the people in those vintage cars were nearly all elderly couples, in the driver's seat were always the men and never the women, and they had rather annoyingly smug expressions while driving. I am afraid that extreme car enthusiasts in general are probably not my kind of people.)

This may not be the prettiest plant I could show, but it is of the plant group I work on professionally. Phagnalon sordidum (Asteraceae), a half-shrub of rocky slopes and walls, here seen in the Gorges de Galamus.

Wednesday, May 28, 2014

Europe day 9: Carcassonne

Another big trip today, this time to Carcassonne. I had been there before, in 1999, but did not remember that it was so big, and then probably did not visit the inside of the castle itself.

The city walls. Although this is the quintessential medieval fortified town, it appears to me that it was rarely useful. After the Roman empire collapsed, the town was conquered by the Visigoths, the Arabs and the Franks. Later, during the aforementioned Cathar crusade, it surrendered to the crusader army. Ironically, one of the rare cases where the fortifications worked was when the Cathar lord tried to retake his castle from the Crusaders a few years later...

City fortifications as seen when entering through the Narbonne gate. There were two portcullises operated from two separate rooms - bribing only one soldier wouldn't work!

This one shows a nice view from the inner castle over the fortifications down to the new city. I particularly like the tower in the centre of the photograph. According to information provided during the tour it dates back to late Roman times as can be seen from its U-shaped foundations: flat towards the town, rounded towards the outside. Also, Roman defensive towers still had larger windows than later Medieval towers.

Another historic town we stopped at is Lagrasse. It has an abbey ruin, but depicted here are a bridge and the outer houses.

On a nature walk near Lagrasse we found this Ruta graveolens angustifolia (Rutaceae) with its intricately fringed flowers. It is a close relative of the traditional aromatic plant Ruta graveolens, and although a herb it is of the same family as oranges and lemons. (Update: Le oops.)

Tuesday, May 27, 2014

Europe day 8: Various ruins

Today we made a trip to the coast to escape the rain. Along the way we went for a short walk in the Garrigue and visited two other sites.

This is the first one, the ruins of the village of Perillos which was deserted about a century ago. Recently work has begun to restore some of the houses such as the one just visible in the upper left corner of the picture, but the atmosphere was still somewhat strange.

Nearby is the ruin of the Chateau de Opoul, here seen from the car park below it. It is much less intact than the previous castle we visited.

Still, the toilet appears to be just as functional as it was hundreds of years ago. But that is probably partly because it is fairly low tech: a hole in a seat jutting out just past the castle wall.

The caste commanded a great view across the valley and towards the Mediterranean Sea. In the background the village of Opoul.

Around the castle I was glad to see Leuzea conifera (Asteraceae) starting to flower. The German name of this low-growing daisy is Zapfenkopf, or cone-head. At first sight it looks as if it might be an apomorphic segregate of Centaurea. Will have to look up if it is actually nested withing that genus.

Saturday, May 24, 2014

Europe day 4

Walked from Lanet to Mouthoumet and back today and am pretty tired now. Either just not used to it any more or still jetlagged, don't know what.

In Lanet the houses and lanes form an intricate maze. Old French villages can be very charming. Note sunbathing cat on the wall to the right.

Lanet as seen from above, from the slopes above the village towards Mouthoumet.

The high plain between the two villages, at approximately 500 m.a.s.l., with a view towards the snow-capped Pyrenees in the distance.

A patch of wild thyme along the way. There were, of course, many more flowers but some of them I don't know the name of yet. I will save them for future botany pictures.

My mother in law made Chevre Chaud yesterday evening. Goat's cheese wrapped in bacon and seasoned with Herbes de Provence, accompanied with seasoned tomatoes. Baked in oven at 220C for 20 min. Served with bread. Simple but delicious.

Friday, May 23, 2014

Europe day 3: Chateau de Puivert

Today we visited the Labyrinthe Vert near Nebias and afterwards the Chateau de Puivert. The former is an amazing area of forest with stunning rock formations but sadly characterised by perennial half-shade, making it hard to get decent pictures with my camera. The following are therefore all either plants or photographs of the castle ruin.

The Chateau de Puivert is one of the many castle ruins in the area that played a role in the Cathar wars. This one was conquered by the crusaders after three days and four nights of fighting.

It was inhabited until the French revolution and has been extensively restored in the last few decades. It was used as setting for several movies, probably partly due to the relatively good state of repair of its main towers and partly due to its accessibility.

Inside there is a small exhibit of medieval items - mostly replicas as far as I can tell. (I know very little French.) There is a suit of armor and a few helmets, instruments, official seals, and some furniture.

It is much easier to see orchids in the Corbieres than in Germany, for example. The above is perhaps one of the prettiest European orchids (or at least that is my opinion) but also a relatively common one. Orchis ustulata (Orchidaceae).

Not an orchid but also an intricately built, zygomorphic flower: Polygala (Polygalaceae). Don't know the species, unfortunately.

Thursday, May 22, 2014

Europe day 2: Cascades de l'Orbieu

Yesterday we arrived in France, and so it is unsurprising that the most dominant feature of today is jetlag. We are taking it slow. However, we made a few small walks in the vicinity.

The above picture shows what we might call the Central Business District of the village we are staying in. Lanet has approximately 60 permanent inhabitants and is surrounded by a few paddocks and lots of awesome forest, mostly of Quercus ilex, Quercus pubescens, Erica arborea and Buxus sempervirens.

An applemint (Mentha suaveolens, Lamiaceae) clogging up a waterspout on a wall in the village. I wonder how the seed got there. And I wonder what happens 'upstream' if there is strong rain.

The endpoint of our last walk today, the cascades of the Orbieu near the old watermill ruins. It was very foggy, and consequently I found it very difficult to take decent pictures, but this one does capture the atmosphere.

The river below the cascades. Although the area is in the rain shadow of the Pyrennees and accordingly dry, it is perennially wet in this particular location. The vegetation is dominated by mosses and ferns, for example Phyllitis scolopendrium, Polypodium australe and Asplenium trichomanes.

Finally, and to end on a very botanical note, a 'princess' my wife made for our daughter from a poppy flower and grass.

Saturday, May 17, 2014

Public service announcement

The next four weeks I will be travelling in Europe, so updates will become sporadic. On the other hand, when I update I will have nice pictures of plants and landscapes. It is spring there, after all.

Matrix Representation Parsimony supertrees

Continuing, for the moment, my little series of posts on the use of parsimony methods in phylogenetics and biogeography, we come to the topic of supertrees.

Some phylogenetic studies deal with higher level groups. For example, one might see an evolutionary tree of the land vertebrates or of the land plants. But in those cases the sampling of the individual groups is very restricted, so that a whole family of mammals or a whole order of plants might be represented with only one terminal.

Other studies deal with more fine scale relationships. For example, there are publications only on the phylogeny of one medium size genus of daisies or one genus of birds. In this case the species within the genera in question are well sampled (hopefully complete or nearly so), but obviously everything outside the study group is represented by only a few close relatives.

At some point one might now want to put all of this information together to arrive at the complete tree of life or, perhaps less ambitiously, at a complete evolutionary tree of all birds or of all flowering plants. How can we take all these individual studies, all dealing with different species and often using very different types of data, and get one tree out of them?

There are two main approaches. It should be obvious that both necessarily require that there is some overlap between the various trees.

Thursday, May 15, 2014

Botany picture #156: Senecio macroglossus

Senecio macroglossus (Asteraceae), New South Wales, 2014. I saw this weird species over Easter and could not figure it out at first although I was sure it must be a member of the tribe Senecioneae. Now a colleague at the herbarium has pointed me in the right direction. This daisy is a vine or liana with stunningly ivy-like leaves (visible see in the upper left corner) and large yellow flowering heads. It is a native of South Africa but has been introduced to coastal Australia as an ornamental. In Canberra it would not grow as it gets too cold.

Tuesday, May 13, 2014

Weird Christian pamphlet, part 2

The fourth and last page of the religious pamphlet we found in our letterbox deals with the mark of the beast.
The Mark of the Beast (Verichip)
"So that no one could buy or sell unless he had the mark, which is the name of the beast or the number of his name. This calls for wisdom. If anyone has insight, let him calculate the number of the beast, for it is man's number. his number is 666"
It is surely not an insight original to me that the author of Revelation appears to have been a bit incoherent. This stuff just doesn't make any sense.
Soon money will be useless and in place of it, the will be put on the forehead, or on his right hand, this will be the only way to buy and sell. Leading edge biometrics technology is already being tested in various parts of the world. We beg you dear friends; do not ever receive any kind of implants used as personal tracking LD. "it you receive it on your right hand or forehead you will go to Hell and suffer forever!"
I have no idea what an LD is, but it is clear what the pamphlet author is aiming at here. They believe that a personal identification microchip formerly called VeriChip and now PositiveID is the mark of the beast mentioned in Revelation, that soon everybody will need to get one implanted into their head or right hand, and that those who have it implanted will go to hell.

The first and most obvious problem I see for this prediction is that VeriChip was not actually ever intended to be implanted into either of those two places on the body but instead into the arm above the elbow. It is also just plain unrealistic to assume that people would, or could, ever be forced to have it implanted. Even if there were no Christians to protest because they connect it with the mark of the beast, most of us would still be squicked out by the idea and consider it a massive violation of our bodily autonomy. Interestingly, in reality such violations are generally only possible if they find a religious justification...
A third angel followed them and said in a loud voice:
"If anyone worships the beast and his image and receives his mark on the forehead or on the hand, he, too, will drink of the wine of God's fury, which has been poured full strength into the cup of his wrath. he will be tor-mented with burning sulfur in the presence of the holy angels and of the Lamb. And the smoke of their torment rises for ever and ever. There is no rest day or night for those who wor-ship the beast and his image, or for anyone who receives the mark of his name." (Rev.14:9-11)
This paragraph then is a bit puzzling because it implies that what brings God's wrath upon us is receiving the mark AND worshipping the beast, implying that if one is merely forced to receive the mark but does not worship the beast one might be fine. At least that is my plain reading here, and it makes sense that a benevolent and just deity would not punish their followers for having been forced into something. But well, that is just my understanding; perhaps religious logic is just different from standard logic...

Monday, May 12, 2014

Weird Christian pamphlet, part 1

My wife recently found a small flyer in our letterbox that had apparently been distributed to all the neighbourhood. Interestingly, it does not contain any address, it does not advertise a book or anything else one is supposed to buy, and it does not promote any specific church. It seems as if the author really, truly believes what they wrote and merely aims to convince people instead of trying to sell them a membership or something like that.

I find it fairly interesting, perhaps mostly because I have rarely interacted with believers like the author, and find it very hard to understand them. The title page consists mostly of a garish, kitschy picture of numerous white-robed, white-skinned men on white horses being led by a face-less, red-robed person raising a sword. Because there is something that looks a bit like the eye of Sauron in the background I thought at first they had stolen the picture from some old edition of the Lord of the Rings, but on further consideration it is probably meant to be the sun with a bit of a smudge in front of it.

Under the kitsch we find this piece of text, with the first line massive and the subsequent ones so small as to be barely legible:
The Second Coming of Jesus Christ
For the Lord Himself will descend from heaven with a shout, with the voice of an archangel, and with the trumpet of God. And the dead in Christ will rise first. Then we who are alive and remain shall be caught up together with them in the clouds to meet the Lord in the air. And thus we shall always be with the Lord.
1 Thessalonians 4/16-17
So the pamphlet is obviously about the rapture. This should be fun.

Saturday, May 10, 2014

Botany picture #155: Wild carrot

Daucus carota (Apiaceae), Germany, 2007. One of the nice things about maintaining an active interest in nature is knowing what the vegetables and fruits we grow in our gardens or get from the market actually looked like before our ancestors started breeding them. In many cases one wonders why they bothered; the rootstock of a wild carrot, shown here in fruit, is not actually that attractive-looking. But I guess one had to start somewhere, and if there isn't anything better...

But that just means we should be all the more grateful to our neolithic ancestors for painstakingly selecting crop plants generation after generation to be more palatable and productive.

Thursday, May 8, 2014

Scientific models are not actually some obscure mystery

Just a quick one on science communication.

Via Pharyngula I learned of a piece in the Guardian, The top ten global warming 'skeptic' arguments answered. Dana Nuccitelli replies to a number of claims or questions made by one of the few climate scientists who still doubt human-caused climate change.

Some of those arguments are actually very twee, and the rebuttals are accordingly amusing, as in the case where the 'skeptic' asks "how do scientists expect to be taken seriously when their theory is supported by both floods AND droughts?" I guess if faced with a breakdown of cargo transportation he would be just as confused why there can be food shortages in one area but undelivered produce rotting in the other - surely it has to be either-or, amirite? Guess stuff like that is complicated.

But as funny as it is, there was one minor point that annoyed me a bit, and that is the answer to the claim that we cannot trust climate models, which went like this:
Climate models have accurately reproduced the past, but let's put them aside for a moment. We don't need climate models to project future global warming. We know from past climate change events the planet will warm between about 1.5 and 4.5°C from the increased greenhouse effect of a doubling of atmospheric carbon dioxide
Excuse me if I am wrong (because I am only a scientist), but it seems to me that the expectation of 1.5 to 4.5°C in warming for each doubling of CO2 is, well, a model. It is a very simple model, but it is a model, because it is a mathematical description of the behavior of a system.

What we see in the Guardian piece is unfortunately rather typical of the public discussion of science. Science is treated as some kind of mystical process happening in the ivory tower but inaccessible to Jane Doe and Joe McAverage. In reality, science is nothing but a formalized version of what everybody does in their daily lives as long as they are unencumbered by religious or ideological blinkers: Accepting the simplest explanation over unnecessarily convoluted ones, testing different ideas against observable reality, demanding exceptional proof for exceptional claims, and so on.

And yes, modelling. Intuitively, we all do it every day. If you are a teacher or lecturer, you may, for example, know from experience that you can grade three student course papers of a certain type in one hour. You would then perhaps assume that you can achieve the generalized outcome of
student papers graded = 3 x time invested in hours.
That is a simple model. In reality, you will find that you get tired and less efficient if you keep on going for too long without breaks. You may then want to adjust this formula to take into account that the factor of papers per hour diminishes over time, so that you may only get eight done in three hours. This would be a slightly more sophisticated model, but the principle is still the same. You put the hours into the model and you get the expected number of graded papers out.

Likewise, really sophisticated computer modelling of climate change probably involves many factors. I am not an expert in that area, but I would expect that CO2, water vapor, cloud formation, ocean temperatures, methane, and planetary albedo all play a role, plus many others. And then there might be positive and negative feed-backs in the model; for example, higher temperature may lead to more water vapor as more water evaporates, and because water itself is a greenhouse gas it may lead to even more warming, etc.

But all that complexity of the sophisticated models does not mean that "ca. 3°C per doubling of CO2" is not also a model. Heck, even the position "there is no significant influence of CO2 on climate" is a climate model, so the position that no models can be trusted is self-refuting!

And this is then what is frustrating. When faced with the usual denialist's canard that you cannot trust any models anyway, most people immediately either grant that argument or, as in this case, change the topic after a flat assertion, so that the on-lookers will walk away with the absurd impression that modelling is indeed an obscurantist, useless egghead's plaything. Instead, we should make an effort to demystify the concept of modelling and try to explain what that word actually means.

Scientific models are really only formalized versions of what all of us constantly rely on to predict the behavior of the world around us. In fact, there is simply no way to even discuss the dynamic behavior of any system - be it a factory, a nation's economy, a human asking for a diet plan, or the global climate - without using models, at least very simplistic ones.

Tuesday, May 6, 2014

Botany picture #154: Rehmannia angulata

Rehmannia angulata (apparently now Orobanchaceae?), Botanic Garden of Zurich, 2009. This is a herbaceous annual species. Despite the fact that it has to be newly raised from seed every year, it is very popular in European botanic gardens. No wonder why - the flowers are unusually large and pretty.

Monday, May 5, 2014

Thomas Covenant the Unbeliever

After reading about the fantasy series and deciding that it sounded interesting, I picked up the first three volumes of Stephen R. Donaldson's The Chronicles of Thomas Covenant at a recent book fair. I have now read most of the first volume and have to confess I will probably give up on it.

The reason why I got interested in the first place is also the greatest strength of the books: their protagonist. Thomas Covenant is not your average fantasy hero. He is a man of our world who gets sucked into "The Land", the magical parallel universe in which most of the story takes place. In our world, he is a leper who has been deserted by his family and is shunned by his entire community. In The Land, he is The Chosen One and venerated by all the forces of Good, and he finds that hard to deal with.

Covenant oscillates between willingness to accept what happens to him as real, the conviction that he is dreaming while in a coma, and a fear of going insane. (Thus the self-chosen title "Unbeliever".) This is worsened by the training he went through when his disease was first discovered, where he was conditioned to accept his leprosy as untreatable and focus on containing it, because of course in magical land he gets healed magically, and he is afraid of believing that in case it turns out to have been a dream.

On the other hand, Covenant is not what we would call a nice person. Despite his friendly and awed reception by the inhabitants of The Land, he is constantly surly, hostile and culturally insensitive towards them and, worst of all, commits a terrible crime against the very first person to befriend him. The reader finds themselves in the odd position of being repulsed by Covenant's character but sympathising with him for the terrible disease and rejection he experienced in his own world; exasperated at his boorish behaviour but at the same time rooting for him because he is the only hope the good guys have to save their world from ruin. One-dimensional he isn't - he is perhaps one of the most interesting characters in fantasy literature.

So what annoys me so much then that I am giving up on the books?

Saturday, May 3, 2014

Botany picture #153: Lycopus australis

It was with great pleasure that I finally encountered Lycopus australis (Lamiaceae) for the first time on the Easter weekend. It is not a very attractive plant, and honestly it does not look all that different from L. europaeus in Germany, but I just really like Lamiaceae and was a bit disappointed I had not found it during my time in Australia so far. Like the European congener, this plant likes open, wet areas.

Thursday, May 1, 2014

Printable solar cells

To allay my notorious pessimism about the future, I went to a talk today. It was about printable solar cells, presented by Scott Watkins, the very same CSIRO scientist featured in the linked news item.

And they are truly amazing. Much cheaper to produce than normal silicon solar panels, flexible (he gave some to the audience to feel), and very simple in their internal structure. Essentially the material scientists just print two layers onto a plastic sheet: first a polymer mixture, then a silver lattice that takes off the power.

In small experimental formats they have achieved the same efficiency as standard silicon solar cells; in larger formats, efficiency is still considerably lower, but they have various polymers to play around with, and they have not even tried how the best mixtures they have already developed work when scaled up, so there is still a lot of potential for improvement. Because so many different polymers can be employed, it is also possible to tailor the printable solar cells to different light wavelengths.

Apparently even in the best case they will most likely not achieve the lifetime of thick and solid silicon solar panels, but again, they will be considerably cheaper. Once the research consortium has settled on the best materials for efficiency and durability, this will have enormous potential.

There is, however, one possible irony: The plastic that the solar cells are printed on, and the polymers themselves, are made from oil. Perversely, that means that the more oil we waste for cars and heating now, the more difficult it will be to produce this type of solar cell in, say, 2050; and the same for any other type of plastic, for all their various uses. Okay, the outlook is not entirely bleak, because some polymers can be made from biomass, but that will be more difficult and use land that could otherwise produce food.


In other news, and certainly completely unrelated to the question of our distressing overuse of petrochemicals, today somebody incredulously asked me if I really rode the bike to work every day, even now in the "cold" "winter" here in Canberra.

Well, yes. It is one hour of exercise every day (30 min each way), with the added benefits of saving money, saving the aforementioned resources, and not getting a fit while standing in the traffic jams on Mouat Street and Northbourne.

Also, it is not cold, nor has Canberra got a winter. I'd say it has four months of what would be late autumn in Germany followed immediately by spring. (Which might be a reason why no native trees have ever evolved to be deciduous.) And of course I also rode my bicycle to university when it was -10C back in Germany. There is no wrong weather, only wrong clothes, and it is not the weather's fault if Australians believe that they should be able to wear shorts and flip-flops at all times.

No offence meant. Just saying.