Botany picture #137: Lomatia silaifolia

Lomatia silaifolia (Proteaceae), New South Wales, 2014. This final picture from our recent field trip to the Blue Mountains shows a rather small Proteaceae that was in full bloom on a recently logged forest area. The plants were less than 1.5 m in height.

No arguments from authority please, even if it is Charles Darwin

Continuing with my ruminations on Richard Zander's Framework. Another thing that got me when reading the book was how often proponents of paraphyletic taxa claim that Charles Darwin was on their side.

In contrast to Zander, who very openly cites the Origin's chapter on classification for support, many of them do so through code phrases; they will write "evolution is descent with modification" and then assume the matter to be decided in favour of paraphyly. Personally, I don't quite get how that definition is supposed to be an argument against cladism anyway. But they think it is, and they think it will impress people because it is supposedly Darwin's own definition of evolution, and he is the authority, amirite?

Botany picture #136: Persoonia levis

Persoonia levis (Proteaceae), New South Wales, 2014. This species surprised us with its large leaves reminiscent of wattle (Acacia) phyllodes.

Why we don't consider supraspecific taxa as ancestral to others

I am currently reading Richard Zander's recently published book A Framework for a Post-Phylogenetic Systematics. As a cladist, phylogeneticist and regular user of molecular sequence data I would call the work a target rich environment and could write quite a lot about it. The problem is, it comes in at 214 pages and is written in an extremely dense, jargon-laden style. Discussing it in a way that does it justice would require an effort similar to Slacktivist's famous deconstruction of the Left Behind novels or Adam Lee's page-by-page review of Atlas Shrugged.

I am neither willing nor able to invest that amount of time, and surely much fewer people would find such an enterprise interesting enough to follow it than in the above two cases. What I will do, therefore, is limit myself to a few unsystematic discussions of individual topics or arguments encountered while reading the Framework. Today we will explore what appears to be its author's greatest frustration with phylogenetic systematics.

Interestingly, every proponent of paraphyletic taxa in botany has a different main argument. Elvira Hörandl, for example, is convinced that 'evolutionary' classifications have greater information content than phylogenetic systems. The late Richard Brummitt argued that Linnean binary taxonomy and phylogenetic systematics are incompatible when we try to classify ancestors. And Richard Zander finds it simply unacceptable that phylogenetic systematics does not allow the treatment of supraspecific taxa as ancestral to others at the same or higher rank.

Botany picture #135: Persoonia mollis

Persoonia mollis (Proteaceae), New South Wales, 2014. One thing that struck me in the Blue Mountains was how many species of Persoonia there are. Of course, their flowers all look more or less the same but they are very variable vegetatively. Some of their fruits are edible although apparently very astringent.

Are we our bodies?

In a recent discussion on another blog somebody claimed that most people would not identify with their bodies but instead with their consciousness or (if they are inclined to give it a supernatural phrasing) with their souls*:

Alex, I can understand your perspective and there may be a considerable number who consider themselves “their whole body”, but I think most people have the conception that they are the consciousness that inhabits and wills the body.
The illusion of separateness from our body I think is rather strong. You may argue that this is just an illusion and you would be completely correct. But I would respond with the concept of soul which seems to be a popular concept throughout the world, not universal but something quite like it probably is for a majority of the human race. This concept suggests that there is a separate conscious entity that is distinct from the body. Why is this an almost universal concept, well the illusion the illusion that we are a separate homunculus is very strong. So I think those who support the idea of the self being defined as the part of the body/mind that is conscious and self aware have the stronger case.
Another thought experiment that will put this in better perspective. It we were able to perfectly record and make an exact copy of your nervous system and then simulate it in a sufficiently advanced computer-like device, I would argue that the simulation would have an experience and that experience could be labeled “you”. Conversely, If we used an extremely potent general anesthesia that precluded any awareness yet did no damage either to your brain or body would “you” still exist?

 I believe that both the assumption that most people consider themselves to be something immaterial living in the body and, to the degree that some people actually do believe that, the reasons for the belief are wrong.

Botany picture #134: Eucalyptus bicostata

Today I was lucky enough to join a tour of the Australian National Wildlife Collection, one of the country's premier biodiversity research collections. It is particularly renowned for its holdings of bird specimens and of frozen tissue that can be used for DNA extractions but it also features collections of mammal, lizard and amphibian specimens as well as bird eggs and nests.

Between the building and the car park stands this fine tree which a colleague identified as Eucalyptus bicostata (Myrtaceae).

And this is why I decided to post it: this species has the longest leaves of all Eucalypts. Quite impressive already but apparently they can get even longer.

Inevitability versus contingency in evolution

This third post on evolution will deal with the question of contingency. I will partly recycle, and partly expand upon, my recent comments at Larry Moran's blog.

The question here is this: If evolution had to start all over again, would it result in the same kinds of organisms or in very different ones? Because we cannot actually rerun evolution on this planet, it could also be rephrased as what we would expect life on other planets to look like, either very similar to that on Earth or totally different. But because we cannot see life from other planets either, for now all we have is informed speculation either way.

The discussion is often simplified as being about two sides. On one side are those who are convinced that life as it is currently developed on Earth is inevitable, either for some teleological or religious reason (with humans as a necessary aspect of divine purpose) or because of a strong confidence in the power of selection to force organisms into a few optimal shapes. On  the other are those who believe that life as it is currently developed on Earth is only one of a myriad of completely different and equally probable outcomes, either because that would make life on other worlds more interesting or because they stress the importance of random mutations and genetic drift over that of selection.

But it is obvious that there is really more of a gradient between two poles. Dividing the spectrum into four more or less arbitrary sections, we could imagine the following positions:

Botany picture #133: Tetragonia implexicoma

Tetragonia implexicoma (Aizoaceae), Tasmania, 2013. Better known from their stunning representatives in the deserts of southwestern Africa, the succulent Aizoaceae family also has a few native species on this continent, such as the one above. Like Actites megalocarpa, it is a dune stabilizer, growing across them in dense mats of tangled stems.

... except under some very specific circumstances

In my previous post I argued that evolution does not, as a whole, have any direction or goal, but I qualified that with the claim that there are some circumstances when it does, and when it even makes sense to think in terms of better and worse or more primitive and more advanced solutions to an adaptive problem. So what would those be?

Botany picture #132: Trochocarpa gunnii

Trochocarpa gunnii (Ericaceae), Tasmania, 2013. A group of shrubs standing at the shore of Lake Burbury near Queenstown. The flowers are so small and somewhat hidden between the tangled branches that at first I assumed the plants were not in bloom.

Evolution does not have direction...

After the post spent harrumphing about scala naturae thinking, I should perhaps follow up a bit to explain my understanding of evolution as it relates to questions of teleology and contingency. As so often, do not assume that evolutionary biology is my speciality, but as a phylogeneticist and systematist I cannot avoid having an opinion. Also, this is once more mainly meant to put my thoughts into a coherent form, but maybe somebody will find them helpful or controversial enough to notice.

I would like to make the following points:

1. As a whole, evolution does not have a direction or a goal. Teleological thinking is a severe misunderstanding of evolution. Consequently, there are generally no 'primitive' or 'advanced' species in biology. This one should not be particularly controversial among biologists but it is sometimes disputed among non-biologists.
2. But! There are a few special cases where I find it helpful and justified to think in terms of directionality and more primitive or more advanced solution to an adaptive problem. Again, in a few special cases only, under a set of very specific circumstances.
3. Finally, the question of inevitability versus contingency. There are those who argue that if the tape of history were rewound and played again, evolutionary history would unfold completely differently because every step is contingent on the ones that came before, and thus we would find completely different life forms in an alternate history or, for that matter, on different planets. On the other side there are those who argue that if the tape of history were rewound and played again, things would come out pretty much the same. I lean towards the latter position - to a degree.

Today, let's deal with the first point. I will expand on the other two later.

Botany picture #131: Acacia verticillata

Acacia verticillata (Fabaceae), Tasmania, 2013. Like many Australian Acacias, this one has reduced its ancestrally bipinnate leaves to phyllodes which are merely flattened and expanded petioles. While the diversity in phyllode morphology is stunning, the diversity in flowers and inflorescences in this large genus surely isn't. Basically, they come in yellow and (more rarely) white and in round heads or (more rarely, as in the present case) elongated spikes.

Fairley & Moore's Native Plants of the Sydney Region

During our recent trip to the Blue Mountains I made some use of Fairley & Moore, Native Plants of the Sydney Region. The positive aspects first: It is most helpful for quickly identifying plant species, at least if you already have a bit of an idea of where to start looking, and allowed us to easily figure out what Grevillea or Persoonia we had just run into. I appreciate very much that the plant groups are arranged in a systematic fashion instead of alphabetically as in some other guides I could mention.

More generally speaking, although I need more sophisticated keys for my actual work I love field guides like these, especially of areas I have never had the chance to visit. At home we have, for example, a guide to the Fynbos flora that was kindly brought back from a visit to South Africa by a postdoc during my time in Switzerland and a guide to the flora of Kazakhstan that was a present from a PhD student in Germany. I cannot actually read the latter except for the Latin plant names but I still enjoy having it.

Using the Sydney Region one really for the first time now, however, it occurs to me that this particular specimen of the genre has a few problems from a scientific perspective. For all the following points, note that what I have is the 'revised third edition published in 2010' so it is not as if the book has the excuse of being terribly old.

Von den Blauen Bergen kommen wir...

The last two days I was on a field trip to the Blue Mountains with a colleague and several students. We were mostly searching for the rare and remote 'pagoda daisy' Leucochrysum graminifolium (Asteraceae), a habitat specialist and local endemic of the area north of Lithgow.

This is the habitat: twisted and weirdly shaped sandstone rocks sticking out of the forest. The place was unexpectedly awesome; I came there expecting simply rocky mountain slopes along the road.

Many of the rocks are clearly layered, and often a higher layer is wider than the layer immediately below it. Together with the stair-like appearance of the rock formations this invites a comparison with Asian pagoda style buildings. At any rate, a nearby national park is called Garden of Stones, surely because the strange rock formations are its major attraction.

And we found it! The paper daisy we were searching for grows directly on the rocks, sometimes in cracks, sometimes on a minimal layer of decomposing leaf litter. The individual specimens often have many dead leaves and substantial rootstocks, indicating that once they have managed to occupy one of the few suitable sites on the rocks they do not carelessly give it up again by having a short life cycle. These plants are much more long-lived than most of their congeners.

This is, of course, the more typical kind of Blue Mountains landscape, seen here from Echo Point Lookout in Katoomba, where we stayed the night.

And finally, another Blue Mountain endemic, Grevillea laurifolia (Proteaceae). It is very easy to recognize because it is prostrate, and other prostrate Grevilleas generally have divided leaves.

SeaView

As mentioned in my last post, I have recently stumbled across a really great and handy software tool for molecular phylogenetics. When installing programs on Linux, I sought for an open source alternative to the sequence alignment editor BioEdit that I have been using on Windows since I was an undergrad. The one I found, SeaView, may in some regards be even better.

Weekend trip to Deua NP; Ubuntu

This weekend, as always this time of the year, our suburb was full of inebriated, heavily tattooed man-children who believe that loud noises and inhaling toxic fumes are the most sublime forms of entertainment ever invented, and so we fled the city and went camping in Deua National Park. I have already written about one of its main attractions (the Big Hole), and we went back to the same place, so I do not have much to add.

The Shoalhaven River is perfect for a four year old as it is slow moving and not too deep. We had a great time there both Saturday and Sunday afternoon.

The heath on the way to the Big Hole. As my wife commented, "in Germany you would see two towns and three villages in that direction." One of the main attractions of this country is its relative emptiness due to low population and a high degree of urbanization.

Persoonia (Proteaceae). This genus is a bit different from most other Australian Proteaceae in that it has fleshy fruits - at least some are edible - and apparently lacks the cluster roots that enable other members of the family to survive on very poor soils.

And a Fabaceae whose name I should know because I already saw it in 2010, but it escapes me at the moment. Whatever its name, its combination of Holly leaves and typical pea flower are extremely odd from a Central European perspective...

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Our adventures with Ubuntu continue:

• The GUI does not allow us to change access rights to files. Yes, we could perhaps do that in the terminal but the point is, it should.
• The Privacy tool does not allow us to delete the history. Yes, we could perhaps do that in the terminal but the point is, it should.
• Skype crashes whenever one of our contacts goes online, whenever one of our contacts goes offline, and whenever we answer a call. We can call others though.
• TreeView X, one of the most widely used phylogenetic tree viewers, crashes whenever I try to open a tree. FigTree, an alternative tool for the same purpose, does everything it should except, strangely, converting a tree into a graphic. On the plus side, I found an absolutely awesome freeware program that I may blog about in a few days.
• The virus scanner is very paranoid and considers many harmless files to be threats, including even a few short executables that I programmed myself for a work project in 2012, and they do nothing but write large amounts of randomized data into a text file.

Because several of these issues do not appear to present themselves to colleagues who are using Ubuntu, they might be due to some problems between the OS and our specific computer. Whatever the reason, this needs work.

Botany picture #130: Aristotelia peduncularis

Aristotelia peduncularis (Elaeocarpaceae), Tasmania, 2013. This plant was one of the few disappointments with the online key I have mentioned previously. Although I knew all the traditionally important characters like its flower formula, and although it is extremely distinctive (opposite leaves, and the petals are three-lobed!), I got nowhere. A colleague from the Tasmanian herbarium told me the name of the species when I showed him this picture. An attractive shrub growing in the western rainforests of the island.

Happy New Year

The fireworks in Canberra centre, last night. That was nice, and the first firework our daughter has seen.

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We bought a new computer a few days ago. So far I have perennially been a resigned Windows user - simply because it always seemed to be more trouble installing Ubuntu than dealing with the default operating system, and because I was used to Windows. In other words, laziness.

Boy, did Windows 8 ever change that calculation.

Yes, Ubuntu also has got a few issues, and the newest Microsoft atrocity sure makes it extremely difficult to install it (this is what saved me there), but Windows 8 is simply infuriating in a way that none of the previous versions was. Using it for two minutes at a time flips me into an incoherent rage. Also, Ubuntu is fast, more elegant, more intuitive and much safer.

In other words, I have got enough. At work it is still Windows, but if the IT people ever migrate us to 8 that will also have to change.