Monday, March 30, 2015

Australia's National Arboretum, part 2: Bonsai collection

As mentioned in yesterday's post on the National Arboretum, the National Bonsai and Penjing Collection (NBPC) was one of the main reasons we went there. I would never have the patience to grow a bonsai myself, but I appreciate them as an art form.

Until the opening of the arboretum, the NBPC was located in Commonwealth Park near the city centre. Although that was more easily accessible especially during the annual Floriade, the new premises work well, and it fits the theme of the arboretum.

A significant part of the collection is made up by native plants such as Banksias or, as in the above case, paperbarks.

Bonsai are Japanese miniature trees, but what are penjing? They are in a way the Chinese counterpart, but the Penjing tradition does not focus on single trees but instead entails the construction of miniature landscapes. They often consist of several species of plants, interestingly shaped rocks, and small houses, boats or figurines.

Above a very nice penjing with fruiting and flowering plants of different species. One is reminded of model train sets without the trains.

And finally an example with figurines, in this case of horses. In addition to the plants, the collection also features examples of fossil wood from the Jurassic. All in all well worth a visit.

Sunday, March 29, 2015

Australia's National Arboretum, part 1

Today we had a family outing to the National Arboretum of Australia, as we had been meaning to do for quite some time already. The arboretum only opened in 2013, as it had been built after the devastating 2003 bush fires on what used to be pine plantations.

Most parts of the arboretum are therefore very recent plantings and will only look interesting twenty years from now. Among the few forest elements that are older is the cork oak plantation seen above. It was planted shortly after Canberra's founding to give the city its own supply of cork. Another is a large stand of Himalayan cedars that is now home to a nice barbecuing site and outlook, and unfortunately some pine plantations have also survived the fires.

When I think of the arboretums I have seen in other parts of the world, I see park-like plantings of many different species of trees, often with an ecological or geographic theme: this is the forest of the Appalachian mountains of North America, over here is a typical mountain forest in southern China, and so on. It is therefore somewhat puzzling that the National Arboretum apparently decided that it would simply divide its area into 104 large cells and then plant only one (rarely two) species in each cell.

Seen in the picture above is the cell for the Californian Fan Palm, and as one can see it contains only Californian Fan Palms, and they are planted in straight lines, and the lines are very far apart. I have no idea why anybody would think that this would be of any particular interest to even a very charitable visitor even twenty years from now when the palms are taller. There will be lines and lines of the same type of tree of the same height, without any underlying story to it. How charming. Did the designers never visit other arboreta? Or is this all perhaps merely meant to safeguard genetic resources as opposed to educate the public?

Well, at least the background of the picture also shows that the arboretum provides magnificent views over Canberra...

...which are sadly marred by so-called artwork that looks like scrap metal. I will never understand why it is considered appropriate to clutter botanical gardens and parks that people visit for the plants and flowers with sculptures. Each to their own I guess.

But I don't want to come across as too negative. The so-called village centre depicted above is currently perhaps the greatest attraction. It features a restaurant / café, a shop, a large science exhibit, ...

...the truly awesome pod playground, which our daughter ultimately had to be dragged away from (I mean, just look at it!), and Australia's National Bonsai and Penjing Collection. These last two alone are worth the visit, and because this has already got quite long I will keep the Bonsai collection for another post, perhaps as soon as tomorrow.

Wednesday, March 25, 2015

Yet more funny science spam

Most of them are caught by the spam filters now, and most of the ones that make it through are unremarkable in their mediocrity, but the following two caught my eye:
JACOBS PUBLISHERS - Let your wisdom enkindle others
Is it too much to ask that they avoid gibberish at least in the company motto?
Warm greetings from Jacobs Publishers!
Sometimes I wonder what language it is that they get these flowery greetings from; other spammers write "greetings of the day" or similar. Is it Punjabi, or perhaps Yoruba? Whatever it is, it doesn't sound unpleasant.
We introduce ourselves as Jacobs Publishers, initiated to serve the scientific community. It is an Open access publishing group that publishes peer-reviewed articles related to different aspects of Medical, Life Sciences, Pharma, Chemistry and Engineering. We have initiated a Journal called Jacobs Journal of Environmental Sciences. With relentless efforts of our Editorial team, we have initiated Inaugural Edition for our Jacobs Journal of Environmental Sciences.
Somebody here really, really likes the word initiated - and could probably use a Thesaurus.
We are planning to release the edition in the month of April, 2015.  On this Occasion, we request you to submit your Research Work as manuscripts to our journal, we would request you to invite your colleagues, experts to submit their manuscripts. Manuscript submissions expected date March 31st, 2015.
Request, on the other hand, does not sound as polite any more.
Authors are requested to pay 199 USD as publication charges for Inaugural edition. Payment could be done only after the completion of Peer Review process and acceptance by our esteemed Editorial Board Members.
This is at least surprisingly honest. Many competitors hide the fees until a paper has been submitted.
Amy Alethia
Jacobs Journal of Environmental Sciences
Jacobs Publishers
9600 Great Hills
Trail # 150 w
Austin, Texas
Yeah, right. If this message is the English of somebody from the USA then I am the emperor of China.

The second one is below the fold. Content advice: may trigger seizures.

Sunday, March 22, 2015

Botany picture #197: Darwinia taxifolia

Darwinia taxifolia (Myrtaceae), Jervis Bay, 2014. Most Myrtaceae are fairly easy to recognise, but this is a rather weird-looking genus that will easily confuse the uninitiated. I was surely surprised when I was introduced to it the first time.

Thursday, March 19, 2015

What is the age of a species?

We had journal club today, and I realised that something that I had always considered quite obvious and logical is not as obvious and logical to everybody else. The question here is: how old is a species?

If you are like me, you will visualise the phylogenetic tree of the species and its closest relatives, point to the moment where it diverged from its sister group, and say that that is its age. See the following diagram:

We know today of the existence of species A, C and D, and if we reconstructed the phylogeny I would say that the divergence time of A on the one side and the ancestor of C and D on the other side, marked with the black line and the number 1, is the age of species A.

However, there is a little snag: What if there were side branches on the tree of life that we do not know about because they are now extinct? In the hypothetical case above, there existed a species B for some time but then it died out. So really the age of species A should be the divergence time from B, indicated with the purple line and the number 2. But if we only know about A, C and D, we can at least say that A is at the most as old as indicated by the black line.

So far so good. What I learned today is that there are apparently people who believe that the age of a species is where the gene copies it is carrying or the family lineages inside it coalesce back in time. This is indicated by the red line and the number 3: the yellow gene tree shows that all extant gene copies (of that gene) in species A are derived from an ancestral copy that existed at time 3.

This time would often be much closer to the present than times 2 and 3. In the case of us humans, we are usually inferred to have diverged from the chimpanzee lineage a few million years ago, but the last female and male common ancestors of all of humanity - the individuals from whom we have all inherited our mitochondria and Y chromosomes, respectively - have been inferred to have existed a few ten to hundred thousand years ago. And indeed some people seem to assume that that is then the age of our species. (See also my earlier dissection of the Doomsday Argument.)

When I was reminded of this concept today I couldn't believe that this would make sense to any biologist. Mike Crisp pointed out the first major problem: this coalescence point constantly moves through time as gene lineages and family lineages proliferate and die out again. As one can see even in my little diagram above, there were several earlier times at which the same would have been true. So how can the age of the same species constantly be corrected downwards as it gets older?

Worse, if speciation events are spaced closely in time and effective population sizes are large, it is well possible that coalescence time might actually be in an ancestor of species A instead of itself; this is known as incomplete lineage sorting or ancestral polymorphism. In other words, species A would then be older than its existence as an independent lineage. Surely that is immediately recognisable as nonsensical.

However, Mike also pointed out that (as I would add: in cases where it is after the lineage divergence time that we can infer), this coalescence point provides a lower limit on the age of a species. So it must then at least be as old as that, and it is at most as old as the divergence time from its living relatives.

Saturday, March 14, 2015

Field guide to the native plants of the ACT

A few weeks ago Meredith Cosgrove self-published her Photographic Guide to Native Plants of the Australian Capital Territory.

It is a great field guide, and in my eyes much more useful than the one I used before. Every species is given a full page with several high quality photographs. Importantly, the photographs are not, as all too often, restricted to the flowers but instead cover all identification relevant characters. Thus most species will be shown in flower, in fruit, and with their overall habit, and then there are pictures of other key traits, such as leaf tips in the case of Lomandra or bark in the case of Eucalypts.

About a third of each species profile is taken up by descriptions and notes. At the bottom of each page are little bars that allow the user to check whether some character on the plant they have in front of them falls into the diversity exhibited by the species presented on the page, leaf width or flower size for example. Then there are a little map of the ACT with known occurrences and a density plot showing occurrence along the elevational gradient. All in all a very useful and informative book that will make identification of plants in the Canberra region much easier for plant enthusiasts.

Although I am very happy with it, there are two issues that other people might find unfortunate. One is that the book is restricted in its coverage to dicots and petaloid monocots; in other words, it doesn't include grasses (Poaceae, Cyperaceae, Juncaceae, Restionaceae). The second is that the plants are ordered alphabetically by family. That makes it easy to find something if you already have a bit of botanical knowledge and can recognise something as, say, an Ericaceae, but it will not help those who are totally at sea and just want to browse though all species with white flowers until they find something that looks right. That being said, there is an intuitive tabular key at the beginning that allows the reader to narrow families down by petal number and flower colour. Anyway, I personally prefer the systematic structure that has all members of one taxonomic group together.

The guide is also affordable at (Australian) $45, and with its A5 format it fits comfortably into a bush-walker's backpack. More information can be found at the publication website.

Thursday, March 12, 2015


The following is, once more, my personal opinion and not necessarily that of my employer, colleagues, friends, family or pot plants. Also, I do not claim to be an expert on moral philosophy or theology.

Continuing my readings of Thomist theologian-philosopher Edward Feser suggested by commenter Cale, I have decided to tackle the Euthyphro dilemma next, out of genuine personal interest. (I will probably rue leaving the posts I find least interesting for last...)

Admittedly, Feser's real topic in the linked post is whether god has, as he puts it, obligations to us, which he answers with no. But I find that much less interesting than the religious replies to Euthyphro. For what it is worth, I see two possible answers to his question. From an intuitive, human perspective it seems fairly obvious that somebody has a responsibility for what they cause and create, and thus a hypothetical creator-god would have responsibility for us. Stepping outside of everyday moral intuition and trying to justify that responsibility from first principles, however, I come up empty-handed because I personally do not see any way to bridge the is-ought gap. But that means merely that ethics and moral imperatives are made up by humans, leaving us again with the human intuition that says that you have a responsibility for your creations.

Anyway, Euthyphro - what is it again? It was Plato's (or supposedly Socrates') response to divine command theory, the idea that our moral compass can only be derived from the gods. I understand that in the original text, which I admittedly have not read, the discussion was rather more complicated, but it boils down to the question whether something is good because the gods command it or whether something is good independently of whether they command it or not.

Monday, March 9, 2015

Student fees and the resulting incentive structure

The following is, once more, my personal opinion and not necessarily that of my employer, colleagues, friends, family or pot plants. Also, I do not claim to be an expert on economics or education management.

Parts of the blogosphere that I am reading are discussing the phenomenon of students hiring ghost-writers to fraudulently provide them with essays they need to get credit in university, and even Ph.D. theses. One commenter provided a link to a nauseating article from 2010 in which an alleged ghost-writer describes his work.

Some commenters then and today have wondered why the professors and lecturers find it hard to identify the fraudulent papers, and why the universities do not throw the book at the cheaters. A few of the replies cite their heavy workload and suchlike.

But instead this made me think of the financial 'industry'. Imagine, purely hypothetically, you are a bank that wants to make a quick buck out of handing out mortgages to people who you know will not be able to pay them off and then selling them off, meaning that somebody else will be holding them when it all comes crashing down while you walk away with profit.

Of course, investors would not buy your mortgage package unless they believed that it was a good investment. So you turn to ratings agencies to rate the investment quality of your product. And here is the kicker: you, who are interested in getting good ratings, pay the ratings agency, which one assumes would have to be interested in being asked to certify for you again in the future. Not that anybody would behave in that fashion, haha, but if, purely hypothetically, they did behave like that, there would be a bit of a conflict of interest here, right?

And unfortunately I wonder if the same does not apply to universities that have to finance themselves mostly through student fees, either because they are private to start with or because they are public but the government has cut too much of their funding. A university is like a ratings agency for students, so what happens if they get paid per student? Every student who gets thrown out of a course for cheating is one fee-paying customer less. Every student who enrols at a different university because this one has built the reputation of being tough and demanding high standards of its students is one fee-paying customer less.

In a system financed by student fees, the incentives for the university would appear to work towards waving the students through no matter how bad they are or what they do. As I see it, either you practise grade inflation and shut your eyes or you will lose customers and thus your income and, in the long run, your job. I am not saying that it is quite as simple as that, because clearly there are other considerations such as the massive endowments of some elite universities in the USA, and some people will have a stronger backbone than others, etc., but still the incentive structure is a problematic one.

Incentives matter. They can make people misbehave who would, under a different incentive structure, have behaved in a perfectly moral fashion. In other words, financing education through fees instead of taxes seems like a tremendously bad idea to me, at least if we want to have a system in which the universities are highly motivated to penalise cheaters and to maintain high standards.

(Of course, libertarians and other free market faithful would assume and argue that it is in the interest of universities to crack down on cheaters because they need a good academic reputation. But still there are two things that the university wants: money and reputation. So what to do if there is a tension between the two? Consider: if you do not crack down you may potentially damage your reputation later if the fraud is discovered, but if you do crack down you are guaranteed to lose paying customers very soon. Do the math.)

Friday, March 6, 2015

Botany picture #196: Picris angustifolia

Admittedly most of the Cichorieae (members of the lettuce and dandelion tribe of the Asteraceae) look kinda the same at first sight, but still the native representatives in Australia are seriously under-appreciated. And, in fact, with the exception of the 'yam daisy' Microseris people usually don't even know them and assume they must be weeds.

In the case of the genus Picris pretty much the whole scientific community assumed that there was only one introduced weedy species on the continent until as late as the end of the 20th century (!) when Walter Lack and Sebastian Holzapfel identified several native representatives (and found that the introduced one whose name had been applied to them had not actually been able to establish itself in the long run). Unfortunately one of the native species is already extinct because between the mid-19th century collection of its first herbarium samples and the realisation that it is a distinct taxon somebody built the city of Perth on top of its rather restricted area of distribution.

These are the fruits of a luckier and more widespread congener, Picris angustifolia (Asteraceae), from Mt Franklin Road two weeks ago. Note the beautifully feathery pappus which, however, has a tendency to fall off, and the intricate surface structure of the cypselas themselves.

The way the whole group is being neglected compared with other native Asteraceae can hardly be demonstrated more clearly than by the observation that even this local species does not appear to be in cultivation in our botanic garden; and while there is mention of a previous accession in the seed bank database it was from 1947 and is probably not extant. Well, that is going to be rectified now as I handed the fruits in the above picture plus a couple dozen more over to the seed bank. Maybe soon we can have it growing in the ANBG, and perhaps the guides and rangers can tell visitors the story of "the weed that was not", as the linked paper puts it.

Tuesday, March 3, 2015

Botany picture #195: Polyscias sambucifolia

As long as it still isn't winter, I can continue with local plants, but soon it will be back to my collection of European and South American pictures. Here from our recent trip to the mountains, Polyscias sambucifolia (Araliaceae). The flowers are small and greenish, but the fruits are quite attractive.

Sunday, March 1, 2015

Parsimony analysis in TNT using the command line version

I guess I can just as well make it a habit to blog some advice whenever I have dealt with a recalcitrant piece of software. Today: Tree analysis using New Technology (TNT).

As I have mentioned before, there are four main ways of inferring phylogenetic trees of evolutionary relationships:
  • Distance/clustering analysis. This is not really a phylogenetic analysis in the strict sense but merely clusters terminals by their similarity, but on the plus side clustering is always extremely fast. There are several programs that can do it, including good old PAUP and MEGA.
  • Likelihood analysis. Simplifying a bit one could say it searches for the tree with the best log likelihood score given a model of sequence evolution and the data. Again there are several programs available to do this kind of analysis, including PAUP, MEGA and PHYLIP. Calculating likelihood values across large phylogenetic trees is computationally intensive, and thus they can take quite some time for larger datasets. This is why somebody wrote the software RAxML, which is designed to do complex likelihood searches with seemingly ridiculous speed by cutting a few corners.
  • Bayesian phylogenetics. This approach estimates the posterior probability of phylogenetic relationships with a Marcov Chain Monte Carlo (MCMC) method. Standard software packages for this are MrBayes and BEAST. If you want a quick answer, you are out of luck though, because MCMC always takes time.
  • Parsimony analysis. The logic here is to find the tree with the lowest number of character changes along the branches, under the assumption that, all else being equal, the simplest explanation is the best. It is often considered less sophisticated than the previous two approaches but it comes with less assumptions; I like it that I know where the computer has its hands, so to say. Once more PAUP, MEGA and PHYLIP implement parsimony searches but they are fairly slow for larger datasets.
This is where TNT comes in. Published in 2003 and made free-ware through a subsidy of the Willi Hennig Society in 2007, TNT could be called the RAxML of parsimony analysis. It can take a fairly large dataset and finish the tree search before PAUP has got its shoes on. What is more, in addition to the already fast standard search it implements the innovative search strategies that gave it its New Technology name part, such as the Parsimony Ratchet. When you use these you will know what speed means!

Sadly, the program has a few downsides. First, its input and output formats are rather idiosyncratic. Second, it has a GUI only on the Windows version but not on Mac or Linux, so that you will have to use command line and scripting on the latter two systems. Third, the documentation is unsystematic and unhelpful, making it very hard to figure out how to effectively use the command line and scripting. Actually, that is not quite true; documentation on scripting per se seems to be okay, it is rather the simple standard analyses that aren't explained anywhere.

This is why I am writing this post. I have just done a simple analysis, and I want to spare others the same investment in time and frustration, and I want to be able to look up my own post in the future, especially should some time pass before I use TNT again.