Monday, December 29, 2014

Island endemic genera and phenetics (that special issue)

(The following is the sixth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Following an introduction and the contributions of Lockhart et al., Hörandl, and George, the fifth full paper in the special issue is Stuessy et al.'s “Paraphyly and endemic genera of oceanic islands: Implications for conservation”.

The main argument is quickly summarised, and it has actually already been made before by the same author, only then in a considerably more concise manner (Hörandl & Stuessy, 2010). When new species arrive on oceanic islands via long distance dispersal, in the most extreme cases as a single seed or a single pregnant female, they may find themselves presented with many new possibilities. Some selection pressures from their original habitat may not exist on the island, and there may be unused niches ready for the taking. The new arrivals also undergo a severe genetic bottleneck, carrying only a small fraction of the genetic diversity of the mainland population in themselves.

This means that island colonisers often have the chance of undergoing spectacular adaptive radiations in a short time. Echium and Sonchus in the Canary Islands, fruit flies or the Silver Swords in Hawaii are just some examples. In the words of Stuessy et al.,
Because of the speed of the divergence, it might be that the island genera are genetically not so divergent from the continental relatives, but they are usually very divergent morphologically, hence their recognition at the generic level.
So because they looked superficially very distinctive after their adaptive radiation into new niches, island lineages were traditionally often treated as genera distinct from the mainland genera they evolved out of. With the advent of phylogenetic systematics, however, they are sunk into these mainland genera, so that these island lineages are not island-endemic genera any more; they are just the island's representatives of the widespread mainland genus.

So what? So, according to Stuessy et al., this:
these actions could have a substantial effect on world island conservation.
This is, as far as I can see, as explicit as the paper makes the argument for paraphyletic taxa, but it is still clear what this is about. The idea is undeniably that one should keep island endemic genera because they make a better sell for conservation politics than mere endemic species.

Wednesday, December 24, 2014

Huskisson Mangrove Boardwalk

After today, I can definitely recommend the Mangrove Boardwalk of Huskisson, New South Wales, to any botanically or ecologically interested visitors of the Jervis Bay area.


Both mangrove species of the Sydney area were present: the larger Avicennia marina (Avicenniaceae) with grey lower leaf sides and orange flowers, which is also shown in the above picture, and the smaller Aegiceras corniculatum (Myrsinaceae) with glabrous leaves and white flowers. Unfortunately, the former was only in bud and the latter was mostly just past flowering. As most readers will probably know, magroves are extremely salt tolerant shrubs or trees growing in coastal mud flats or estuaries.


A particular attraction of the mud flats, and especially to young children, are seven species of crabs. We believe we saw at least three of them, including the green one above which we saw on the decaying wreck of a little rowing boat. There were also various species of fish, but those were harder to photograph.


Less of an attraction, it has to be admitted, were these mosquitoes. They were rather large and could suck an astonishing amount of blood as we found when one was killed after her meal... Note to self: next time, bring mosquito repellent.

Anyway, definitely worth a visit. I had never before seen such a nice and accessible mangrove swamp.

Tuesday, December 23, 2014

Botany picture #188: Lobelia anceps


We are spending the holidays at the coast, where I ran into this little flower. Lobelia anceps (Lobeliaceae) occurs in wet seepages on the coast of eastern Australia.

Monday, December 22, 2014

An eighteen pages long perfect solution fallacy (that special issue on paraphyly)

(The following is the fifth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

As I am looking at the next contribution to Annals of the Missouri Botanical Garden's special issue on how awesome it would be if only we would accept paraphyletic groups as they did in the 1950ies, it seems as if I should start with the following disclaimer.

I want it to be understood that I have the highest respect for the life works of everybody involved, and for their publications other than the one we are currently dealing with. I do not wish to offend, but merely to critically discuss the scientific merits of 'evolutionary' systematics versus phylogenetic systematics, and specifically whether the arguments presented by the former school of thought make any sense. It also needs to be understood that my opinions expressed here are my own and are not necessarily those of my employer, nor those of my line manager, of my colleagues, of my friends, of my relations or, for that matter, of my pot plants. The same applies to all my posts, of course.

With that out of the way: the contribution I will discuss today, The case against the transfer of Dryandra to Banksia (Proteaceae) is … not a terribly well written paper.

For background, several years ago it was found that both molecular and morphological data showed Western Australian Dryandra to be phylogenetically nested within more widespread Banksia. It is no exaggeration to say that a Dryandra is just a Banksia with a shorter inflorescence, and consequently most taxonomists and systematists decided to unite the two genera. However, the “loss” of Dryandra as a distinct genus has left many people profoundly unhappy. One of these people appears to be the author of the present contribution.

Saturday, December 20, 2014

More on trying to use SNAPP

Further to my notes on the BEAST template SNAPP from a few days ago, here is a little issue that people who happen upon this blog via entering SNAPP into a search engine might be interested in:

Check the 'totalcount' values in your XML files before starting the BEAST run.

You would think that if you entered a SNP dataset with the three character states 0, 1 and 2* into BEAUTi, it would recognise three character states and write totalcount="3" into the XML file, wouldn't you?

Well, I thought so too, but apparently it will, at least as version 2.1.3 on my machines, randomly pick either a 2 or a 4. No idea why. Nor do I have any idea how BEAST interprets the 0, 1, 2 states when it only expects two states. What I do know is that you can correct the XML file manually - simply do a search and replace of totalcount="(whatever the wrong number is)" with totalcount="3" -, and that my analyses are even slower now that I have corrected BEAUTi's mistakes. But at least this explains why I got nonsensical results in some cases. Yippee.

Footnote

*) Homozygous for the major allele, heterozygous, and homozygous for the minor allele, respectively.

Wednesday, December 17, 2014

Back to Richard Zander's Framework: about a book review

Richard Zander, the author of the Framework for Post-Phylogenetic Systematics (which I reviewed for a society newsletter, see also my blog posts here, here, here, here and here) is outraged by what he calls a “particularly nasty” review of his book by Andrew Brower in the journal Cladistics. Of course his book was never going to be received well by this bastion of the school of systematics he is most aggressively opposed to, but he complains that the review “lacks understanding and collegial dignity”.

He submitted a supposedly “light-hearted” response to Cladistics but was turned down; and although they may exist somewhere I cannot remember ever having seen a rebuttal to any book review in any journal before, so that does not surprise me. His reply can therefore be found in Phytoneuron, a journal that I had never heard of before. It seems to be an online-only, one man operation, whose review process is described as follows (accessed 17 December 2014):
Submissions will be promptly reviewed for content and style by the editor, based on his own knowledge and expertise. If deemed appropriate or necessary by the editor, or if requested by the author, review by other botanical peers will be sought.
Zander's reply consists mostly of a complaint about Brower's “disparagements” and two arguments by analogy; the latter I found so bizarre that I felt motivated to write this post. First, however, the tone.

Monday, December 15, 2014

Trying to use SNAPP

I really should rewrite my post on species tree methods one of these days. But at the moment I do not have the energy, and so I will simply write a few words on my experience with SNAPP.

Anybody who happens upon my species tree methods post will see that despite being more of a parsimony guy myself I have a lot of praise for BEAST. It is fast (for a Bayesian method) and very user-friendly. "Normal" BEAST is for standard gene tree phylogenetics, *BEAST or starBEAST is the add-on for species tree analyses based on multiple independent genes, and the still fairly novel SNAPP is the add-on for species tree analyses based on Single Nucleotide Polymorphism (SNP) data.

With genomic sequencing, SNPs are only going to become more important for the study of closely related organisms. If you have species that are very recently derived, any individual gene sequence is probably going to be extremely similar between them. This means that the approach of inferring species trees from the reconciliation of multiple gene trees is unlikely to work: instead of gene trees you are likely to get gene "combs", simply unresolved relationships.

There will still be thousands of little individual mutations differentiating your study specimens, but they will be distributed all across their genomes. This is why they are called SNPs: Single Nucleotide Polymorphisms each surrounded by conserved sequence regions.

The idea of SNAPP is now to use the SNPs from multiple samples per species directly to infer the species phylogeny, without any intermediate steps like alignments or gene trees. For this, it uses the coalescent model and the usual Bayesian Marcov Chain Monte Carlo approach. This sounds very attractive, especially after the good experiences with BEAST, and also very rigorous.

Unfortunately, so far my attempts at using SNAPP have been rather frustrating. There are three main issues:
  • SNAPP appears to be rather capricious as to whether it will run at all or whether it will fall over. The only machine on which I can get it to run consistently is our family computer, a Linux machine. On the Windows machine at work it is also very consistent in that it always error messages and crashes.
  • BEAST in general is known to have a problem with missing data although it can at least be tricked into accepting an allele missing for a species. Still, the same problem applies to SNAPP; a colleague had to throw out most of the data and samples he had to get missing data below ca. 5% before he could do an analysis. In my dataset that is just not possible, I'd be left with too few SNPs.
  • Finally, SNAPP is really. Really. Really. Slow. A hundred SNPs, no problem, I can run a decent analysis over a day. Five hundred SNPs? Forget it. Our high performance computing cluster at work did 1,000 generations over a few hours, and I need it to do at least ten million generations; do the math. At home I just tried a dataset reduced to 200 SNPs, and it seems as if it will finish in three months. All that sounds like First World Problems, but the thing is, the whole point of genome-wide SNPs is that you have thousands of them. A SNAPP analysis of my whole dataset is just not going to happen, even if I did not have the missing data issue on top of it.
I will see what I can do, but at the moment this new piece of software seems to be a realistic option only for rather small datasets, on the lines of the Amplified Fragment Length Polymorphisms I generated for my Ph.D. more than a decade ago...

'Evolutionary' classifications still do not have any information content (that special issue on paraphyly)

(The following is the fourth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

(Updated 29 December 2014 to increase clarity and to make the style a bit less strident.)

Next we come to the contribution written by Elvira Hörandl (2014). I could say that the paper is a strange thing, but then again most of them are seeing as how they generally do not fall into the usual categories of publications in my area, either original research or review articles. In the present case, the paper could perhaps most accurately be described as a review article, but one looking back not, as usual, across a rich and productive field that the author now attempts to summarise, but looking back instead onto a single previous publication: a classification of the buttercup genus Ranunculus also published by herself (Hörandl & Emadzade, 2012).

This means that except for lacking the methods section and extensive supplementary material this paper has pretty much the same content as that earlier publication: it describes the same classification and extols it as superior to one that would accept only monophyletic taxa. It contains much rapid-fire criticism of phylogenetic systematics but mostly revolves around two central claims, and it is those two which I will focus on in this post.

Thursday, December 11, 2014

Botany Picture #187: Nertera granadensis


Nertera granadensis (Rubiaceae), Argentina, 2009. This little creeping plant is apparently a popular ornamental as a ground-cover. This picture, however, was taken in the wild near Bariloche.

Tuesday, December 9, 2014

Intelligence is not actually magic

Reading once more a discussion of the singularitarian movement Less Wrong, it occurs to me that the principal mistake of singularitarians is not actually their belief in accelerating and unbounded progress. Yes, they are wrong about that too, but the core mistake is this:

They believe that intelligence is a kind of magic pixie dust that enables the being exhibiting that intelligence to achieve, well, pretty much everything it can imagine.

That is really at the core of their fear of hostile artificial super-intelligence, and of their hope for the fruits of building a friendly artificial super-intelligence. They believe that if somebody builds a sufficiently clever supercomputer then this supercomputer can achieve anything. Immortality. Space flight. Free energy. Exterminating all of humanity. Feeding all of humanity. And a pony.

A simple thought experiment should set this straight. Imagine a small island in the middle of the ocean. It is just a bare rock, without any plants, animals, iron ore, coal or whatever resources beyond rock. Now plop down on this island the superest super-intelligence you can just about imagine, and imagine that it wants to leave the island.

Will it succeed? Well no. How could it? There are no resources whatsoever, and rocks don't swim.

The same principle applies if we swap the island for our planet. It is well possible that no matter how super-intelligent a friendly intelligence is, there will still not be enough resources on this planet to work out a way to provide eight billion humans with a lifestyle that is both comfortable and sustainable.

It is well possible that it is quite simply physically impossible for a fragile biological organism to fly to a distant star and survive the journey, full stop, and that even a super-intelligence could only concede that fact.

It is well possible that immortality, even as "brain-uploading", is an unachievable dream, and that even a super-intelligence could only concede that fact.

It is well possible that fusion power cannot be produced economically outside of a star, and that even a super-intelligence could only concede that fact.

And it is actually pretty likely that an evil artificial super-intelligence could be stopped in its tracks by taking an axe to its power supply, just like the most intelligent human could be knocked out or shot by one of the stupidest.

Because intelligence is not magic pixie dust. It is perhaps best defined as the capability to solve problems efficiently, but it cannot solve unsolvable problems, and it does not somehow make the laws of physics go away.

Monday, December 8, 2014

The word paraphyletic still doesn't apply to groups of sexually reproducing individuals (that special issue on paraphyly)

(The following is the third part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

(Updated 29 December 2014 to increase clarity and to make the style a bit less strident.)

Although I have yet to read through all of them, I can already say that the first proper paper in the special issue, Lockhart et al.'s “We are still learning about the nature of species and their evolutionary relationships”, seems a bit out of place. It focuses mostly on one idea: there might be ongoing gene flow between the entities we currently recognise as species, and therefore the currently used coalescent species tree methods might be inappropriate to reconstruct phylogenies in those situations.

If that were it, one could happily agree, all cladists could happily agree, and we could call it a day. However, this paper was submitted as a contribution to a campaign for the recognition of paraphyletic supraspecific taxa, and so the clear implication is that the observation of occasional introgression between closely related species somehow means we should not classify organisms by their relatedness. The other authors of the special issue will surely cite this paper as supportive of that position over the next few years, and Lockhart et al. must be aware of that.

Saturday, December 6, 2014

Sectarianism


On a little field trip yesterday I saw what must have been the saddest cemetery I ever visited. A straight path across a weedy lawn, and at intervals there were sign posts pointing off to the sides: Catholic; Anglican; Methodist; Jewish; Independent.

Are different sects so icky that the religious have to keep them apart even in death? I am an atheist, but I would not have any problem with being buried between a fundamentalist Muslim and a Scientologist. Who cares? We are all humans.

And that poor Methodist grave. There was but a single one in that area, all alone by itself.

Tuesday, December 2, 2014

Botany picture #186: Melia azedarach


Recently I saw this tree planted along a road and wondered what it was; just a few days later I saw the same species in the Australian National Botanic Garden, and the label next to the stem solved my question. Melia azedarach (Meliaceae), of Australia and south-east Asia, is widely known and, despite its toxicity, frequently planted, but I hope my ignorance of this particular species is excused in the light of my provenance from an area devoid of Meliaceae.

Monday, December 1, 2014

Circular reasoning works because circular reasoning works (that special issue on paraphyly)

(The following is the second part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

The first paper is titled EvolutionarySystematics and Paraphyly: Introduction, and was written by Tod Stuessy and Elvira Hörandl, the organisers of the original IBC symposium. It can be read not only as an introduction to the topic but also a kind of summary of the whole special issue, and thus it might potentially make more sense to discuss it after the others. Also, it is densely packed with a great variety of claims, generally without developing or supporting them, because that job is quite reasonably left to the individual contributions to the special issue. Still, I will follow the sequence of papers as presumably intended by the editors.

Unfortunately, where one can discuss the central argument of more focused papers, in this case due to its nature there is hardly any alternative to going through the piece claim by claim and rebutting them individually, which makes for a less pleasant reading experience.

Saturday, November 29, 2014

Something to be proud of?

Among the popular 'New Atheists' Sam Harris has always one been of the most controversial, probably because he defies easy categorisation.

He promotes equality and human rights and then turns around and advocates the kind of profiling that would target people of certain religions and age groups. He exhorts people to use their capacity for reason and then argues in favour of extremely liberal gun laws using arguments that I at least would call paranoid. He is a neuro-scientist, he believes that science can answer ethical questions, and he rejects compatibilist conceptions of Free Will, but at the same time he promotes spirituality, which is surely a concept heavily contaminated with religious baggage if there ever was one.

The latter is what his newest book is about: Waking Up - A Guide to Spirituality without Religion. I have not read it, nor do I plan to; I need spirituality about as much as a tattoo of a mermaid on my arm. Each to their own I guess.

However, when idly browsing a book store at Wellington Airport yesterday, I was bemused to note that with writing Waking Up Harris has achieved a new placement in book stores: instead of being sorted with popular science as before, he can now be found between the esoterica and self-help books written by people like Deepak Chopra and Oprah Winfrey.

I am not sure he is proud of that association...

Thursday, November 27, 2014

Botany picture #185: Pachystegia insignis


These past three days I have been at the annual conference of the Australasian Systematic Botany Society at Massey University in Palmerston North, New Zealand. Unfortunately, I will not participate in the field trip to the volcanic plateau tomorrow and instead return home. However, at least I have seen a nice native daisy here: Pachystegia insignis (Asteraceae), planted in a flowerbed directly in front of the hall where the conference took place. The name was kindly provided by Ilse Breitwieser.

Tuesday, November 25, 2014

Yay! A special issue all about paraphyly!

(The following is the first part of a series of posts on an Annals of the Missouri Botanical Garden special issue on "Evolutionary Systematics and Paraphyly". All posts in this series are tagged with "that special issue".)

In 2011, the International Botanic Congress, the largest meeting of plant scientists on the planet, and indeed so large a meeting that it is only held every six years or so, took place in Melbourne. Among the symposia organised at the IBC in that year there was one with the title “Evolutionary Systematics and Paraphyly”, chaired by some of the few botanists who still insist that paraphyletic supraspecific taxa should be accepted.

Sadly, I missed that symposium because I went to a more important parallel session. Recently, however, a special issue based on the symposium appeared in the Annals of the Missouri Botanical Garden. Time to blog about phylogenetic systematics again, it seems. My plan is to go through the articles one by one (with the exception of the last one, which for some unfathomable reason appears to be about Pandas and has nothing to do with classification; indeed one wonders whether they mixed up the journal in which that paper was supposed to appear). But before I start, I want to clear my throat, so to say.

Sunday, November 23, 2014

The new daisy section of the Australian National Botanic Gardens

Tomorrow, the new daisy section of the Australian National Botanic Gardens will be opened formally. Sadly, I will miss that ceremony because I will be sitting in an airplane to New Zealand.


I regret this particularly because I have been involved in the planning of this new section right from the start. For the past few years I was a member of the Daisy Working Group meeting regularly to brainstorm, discuss and plan the selection of species and where to source them, the design of the garden and the information signs that should be put up.

My role was of course a rather minor one. I have not the slightest lick of knowledge in horticulture or landscaping and was thus unable to contribute much to the real design part of it. Instead, I was one of several who provided ideas on what plants one could include and what stories one could tell, and in the last stages I checked signs and other information material for its scientific accuracy. I am very proud, however, that the garden is growing two very rare and endemic species from seeds that I contributed.


Knowing that I would miss the opening, I took my family to see the garden this weekend. From the outside, of course, as it is still closed to the public. The landscaping is impressive, with slopes, channels and depressions cleverly designed to provide for very different habitats ranging from dry to boggy, and at the same time to enable a more economical use of rainwater.


While the plants are obviously still young, and the garden has a distinctly "recently planted" feel to it that will surely disappear within a year as plants spread out a bit, it is already admirable in its diversity of form and colour. There are mass displays as well as smaller, raised containers showcasing individual plants; and in due course, there will be shrubs and treelets around the edges.

Worth a visit if you happen to be in Canberra one day - as are the entire Botanic Gardens, of course.

Thursday, November 20, 2014

The Dark Side of the Sun


I have also just recently re-read one of Terry Pratchett's Science Fiction novels, The Dark Side of the Sun. Its message is one that I have always struggled with when it was presented as a more explicit claim: there is no objective view of reality, instead we cannot avoid having a subjective perspective depending on our identity. The scientifically most advanced alien species in the book have realised that they have hit the limits of what they can figure out, and so they try to gather insights from other intelligent species. The Creapii go as far as to recreate the natural environment of other life forms to immerse themselves in it, to try to feel what it is like, for example, to be a human.

This idea that all knowledge is subjective is a very po-mo concept, and I somehow suspect that Pratchett cannot mean it quite to the strictest interpretation. Indeed I can hardly believe that postmodernist scholars can really mean it like that. A water molecule consists of two atoms hydrogen and one atom oxygen. If a Creap, a Phnobe or a Drosk - three types of alien from the novel - examine water, would they find it to consist of three hydrogen atoms instead, or perhaps to contain plutonium? Surely not. Instead of “it has two atoms of hydrogen” they might say “sldjlkjs lksjf l slkfdj lsj fs”, but once we clarify all the definitions and translations we would expect to arrive at the same number of atoms of each kind, because that is just what is observable out there in nature.

By extension the same goes for everything that can be tested or examined empirically. There should be no female or male astronomy, no Jewish or Aryan physics, because the stars are the stars and the Theory of Relativity is either a good description of reality or it isn't.

What there is, if anything, is the good old “what it is like to be a bat” question. In an important sense, we humans will never know what it is like to be a bat, and I will never know what it is like to be a woman. All we can do is contemplate things at a purely intellectual level, such as that bats use echolocation and that women can (usually) become pregnant, but how any of that feels I at least will never be able to truly appreciate.

But there are two things to be considered here. The first is that this is perhaps somewhat regrettable but not really crucial. It is much more important to know the stuff that we can indeed figure out as objective knowledge, the kind of stuff that allows us to heal diseases, build working machines and improve our agriculture, than to know how if feels to be somebody or something that we just plainly aren't.

The second is that it cannot be helped anyway. Even the super-advanced aliens of Pratchett's story must ultimately make do with asking other species about their views. The book ends with everybody talking, listening, exchanging perspectives. And that seems to be all that is really needed.

Wednesday, November 19, 2014

Botany picture #184: Ranunculus lappaceus


There are some genera that appear to be all over the globe, and the buttercup genus Ranunculus is one of them. So even here in Australia one can see a few spring flowers that aren't introduced but still remind one of Central Europe. This is Ranunculus lappaceus (Ranunculaceae), Australian Capital Territory, 2014.

Tuesday, November 18, 2014

Foundation's Edge

Having now also read Asimov's Foundation's Edge, I must once more wonder about the way this author described, and thus presumably must have seen, women. It is really striking how they are introduced:
The clothes they had given her fit surprisingly well and there was no question that she did not look at all ridiculous. Had they pinched in her waist? Lifted her breasts? Or had that just been not particularly noticable in her farmwoman clothing?
Her buttocks were prominent, but not displeasingly so. Her face, of course, remained plain, but when the tan of outdoor life faded and she learned how to care for her complexion, it would not look downright ugly.
Feel dirty already? And this is from one of his late novels, not the 1950ies, and the person whose thoughts we are sharing here is a high ranking scholar of a supposedly equal opportunity organisation whose most capable members specialise in reading each others minds! Another woman is introduced later as follows:
She was small-breasted and narrow-waisted, with hips rounded and full. Her thighs, which were seen in shadow, were generous, but her legs narrowed to graceful ankles. Her hair was dark and shoulder-length, her eyes brown and large, her lips full and slightly asymmetric.
Later she puts herself down a bit with the observation that her buttocks are too fat. Of course, male characters are also described and their level of attractiveness is judged, but the language is considerably less voyeuristic, less focused on details, and thus much less creepy.

The other issue is the philosophy behind the story, and here I should now say:

MASSIVE SPOILERS AHEAD

The whole book is about a decision that has to be made about the future of humanity. There are three options:
  1. The (First) Foundation Federation rules over a third of the galaxy and continues to expand. It is supreme in the natural sciences and engineering and it is democratically governed, but it brings with it the age-old human foibles of expansionism, militarism, corruption and envy, so that there is reason to suspect that it will ultimately repeat the same mistakes that destroyed the galactic empire that ruled before it.
  2. The Second Foundation is a secret society of powerful telepaths and their supporters who have made it their task to clandestinely manipulate the thoughts and emotions of political and military leaders across the galaxy to steer it towards a more stable, more peaceful future than the Federation would normally achieve. True to this paternalistic approach, they are anything but democratic: because nobody knows they exist, one can only become a member by being recruited by one of their agents, and the overlord of the whole organisation selects their (usually his) successor by fiat.
  3. Finally, there is a planet that has developed a hive mind. They are basically the Borg without metal parts and with a healthier complexion. Yes, they claim that they also maintain their individuality in addition to living in total harmony with each other and with nature, but how does that individuality work in practice if you cannot do anything that the rest of the planet doesn't want you to do, down to career choice or food intake? Anyway, their idea is to spread the hive mind across the entire galaxy.
So here we have the three possible futures: either the Federation blasts the other two and builds a new technological civilisation of free but irrational and short-sighted humans, or the telepaths secretly rule and manipulate humanity for the greater good, or all of humanity gets assimilated by the Borg.

And the thing is: we are very clearly supposed to root for the Borg.

That seems like a rather big pill to swallow, and somehow I suspect that I would be on the side of the Federation, even if their current ruler is quite obviously modelled after Margaret Thatcher. At least humans are still allowed to be humans and to make their own choices!

It is also quite interesting how Asimov has the various factions summarise their offers. “Free will”, says the leader of the Federation. “Guidance and peace”, says one of the top telepaths. “Life”, says the hive mind. Now semantic hair splitting about various definitions of Free Will aside, the Federation has, in my eyes, said just the right thing, because self-determination is what it is about. The telepath was probably supposed to stress that they only guide, not rule, but really this comes across as if he was the only one to also mention the downside of choosing them; he should just have said “peace”. Finally, the hive mind is really disingenuous. How are the other two not also life? What is more life about submitting to a hive than about being an individual?

Sorry, but Asimov did not convince me that this book had a happy end.

Sunday, November 16, 2014

Your mileage may vary on certain internet discussion memes

I do consider myself to be an advocate of equality for all, of feminism, and of inclusiveness. However, when reading controversies around these issues on the internet I have to admit to finding myself somewhat alienated by the behaviour and culture of some of the people who aim to promote those very same goals.

The problem is that at least some activists for Social Justice, as apparently for some strange reason equality is called these days in some parts of the internet, appear to have embraced a set of, for want of a better word, memes that carry the risk of inoculating against even legitimate criticism and argument, or which at a minimum can be very two-edged swords.

Again, I am mostly on board with the actual aims: slurs should not be used; under-represented groups should be made to feel welcome, and their representation should be increased; there should be no unearned privileges; everybody should be able to feel safe, everywhere. Really all that stuff should, of course, be obvious. It is what is generally known as "being a civilised person" and "not being evil".

But all of us make mistakes, all the time, and if we are not careful we may find it hard to admit them and instead dig ourselves in. It is thus important that we avoid deliberately equipping ourselves with a set of mental tools that make it even easier for us to deflect criticism without even listening to it.

In addition, any group of like-minded people runs the risk of developing its own memes, or other forms of coded language, that are opaque to outsiders. This allows for easy identification of ingroup members but can be counter-productive in that it makes it harder to convince those who have not already adopted those memes and language.

In particular, I am feeling somewhat uncomfortable when I run into the following:

Wednesday, November 12, 2014

Botany picture #183: Catananche caerulea


Catananche caerulea (Asteraceae), France, 2014. This daisy is a member of the dandelion tribe Lactuceae, most of which pretty much looks like, well, dandelion. It is thus refreshing to see a representative that is not yellow and actually very pretty. Another characteristic of this plant is that the fruiting heads have dry bracts that make a somewhat rustling noise when the head is shaken, thus inspiring the German name Rasselblume.

Sunday, November 9, 2014

Foundation and Empire

After his later work (but earlier in the story time line) Prelude to Foundation, I have now just finished Isaac Asimov's Foundation and Empire (as the original Foundation continues to elude me at the local book fair).

Foundation and Empire is a Science Fiction book that was written in 1952, and boy does it show. Nothing feels as old as old Science Fiction, but in this case it is really the everyday things that I find off-putting.

A psychologist, a renegade trader, a historian and a clown travel through the galaxy in the same space ship. Guess: who has to make the sammiches all the time? Here is a hint: the historian is the only woman on board. I guess you get the picture.

But of course, to complete this picture Asimov also had to include a scene that scarily demonstrates how the true misogynist will never respect a woman no matter what she does. You know the drill. Woman doesn't want to have sex? She's a prude. Okay, now woman wants to have sex? She's a slut. Woman is assertive and outspoken at work? She's a harpy. Okay, now woman is polite and accommodating at work? Well, that just shows that women can't be leaders, and all higher level positions should be reserved for men. Can't win except by not being a woman.

In the present novel, woman is supposed to make sammiches. But when she makes the sammiches, like a good woman ought to do? This is the thanks she gets from her husband and another main character: "Where's Bayta?" - "Setting the table in the diner and picking out a menu - or some such frippery."

And again, that female protagonist is an academic, but here are a few excerpts from her husband introducing her to his father:
His eyes were on Bayta now, and didn't leave. He spoke to her more softly, 'I have the [picture] of you right here - and it's good, but I can see the fellow who took it was an amateur.' [...]

She sat down, crossing her knees, and returned the appreciative stare of this large, ruddy man.

'I know what you are trying to estimate, and I'll help you; Age, twenty-four, height, five-four, weight, one-ten, educational speciality, history.' She noted that he always crooked his stand so as to hide the missing arm.

But now Fran leaned close and said, 'Since you mention it - weight, one-twenty.'

He laughed loudly at her flush. The he said to the company in general, 'You can always tell a woman's weight by her upper arm - with due experience, of course.'
Charming. It is like a new car being discussed by the friends of the buyer, only the car wouldn't be embarrassed by what one says about it.

Also, this is the year tenthousandsomething (or was it twenty?), and everybody smokes. All the time.

Finally, Asimov wants to fill his universe thousands of years in the future with some super-futuristic technology? Easy. He just treats space ships flying across half the galaxy like caravans driving across the USA and calls everything "atomic", be it an engine, a weapon, a shield or a small gadget fitting into the palm of the hand.

Well, he got better. As indicated, Prelude to Foundation was written much later, and it does not come across as quite that dusty. Also, it is better at taking women seriously.

Sunday, November 2, 2014

Molonglo Gorge

Today I was for the first time at Molonglo Gorge, a narrow valley near Queanbeyan. A few impressions:


It was a perfect day for walking - dry and not too hot.


Woody vegetation is dominated by Callitris conifers such as the one sticking out in the above picture, Eucalyptus (obviously) and a few miscellaneous shrubs, often Myrtaceae or Fabaceae. There do not appear to be many Proteaceae in this part of the country, and although the sign at the beginning of the path talked of Casuarina stands we did not really see those either. Maybe we didn't get that far, because...


We haven't seen the end of the path yet because we were too slow and decided to turn back before we got there. We spent too much time looking at plants and taking in the view and, in the case of our daughter, playing at the river's edge. Also, it has to be said that the path is not easy for a five year old.


The native Clematis (Ranunculaceae) this fruit is from grew at the beginning of the path. Clematis fruits are technically achenes because they are one-seeded, dry and indehiscent, but they have a long feathery tail for wind dispersal.

Tuesday, October 28, 2014

Botany picture #182: Lissanthe strigosa


Lissanthe strigosa (Ericaceae), Australian Capital Territory, 2014. Another little heath from the area.

Friday, October 24, 2014

Taxonomy is more important to hunter-gatherers than to farmers

Over the past few days we had a big strategy meeting across the Australian national biological collections: land plants, tree seeds, algae, insects, land vertebrates, and fish. One thing that struck me was the following:

All collections do taxonomic research as part of their core business, that is describing new species, writing identification keys, publishing field guides, compiling lists of accepted names, etc. But whereas in the other five this research is mostly done for the purposes of informing conservation management, biosecurity and weed management, other scientific research, and the general public (e.g. native plant enthusiasts or bird watchers), fish taxonomy is the only one that really has deep-pocketed primary industry interest behind it.  The fishing industry is actually asking and paying for basic taxonomic research.

Why is that the case? Are ichthyologists simply better than botanists or herpetologists at engaging commercial partners? But if you think about it, there could be a much simpler answer: Fishing is the only food sector in which our civilisation is still pretty much at the hunter-gatherer stage.

Yes, there are some fish farms these days, but what mostly happens is that somebody casts their net into the ocean and catches a chaotic mixture of organisms. And then of course they have to know: which of these are edible? Which of these are worth the bother to process them? How do we have to process them? What are their names, so that we can sell them without frustrating the consumer? All that is really taxonomic knowledge.

In other food sectors the situation is much simpler: A farmer will not really be under any doubt that they harvest wheat after sowing wheat, or that the animal going bah on their paddock is a sheep.

If, however, we still obtained our vegetables and fruits the way we obtain our fish, we would have somebody come to the market with a big bag of stuff that they collected in the bush; they would tip it out, and then they would wonder: Is this berry edible or is it poisonous? What is the name of this weird bulb I have never seen before, and what can it be used for?  Are these two tubers the same species? What should I name this type of nut so that the buyer knows what they get?

If that were the case, we would also see more direct "industry" interest in plant taxonomy. Although of course a society operating like that relies on painful trial-and-error instead of formal scientific studies and on personal instruction instead of a four volume print flora, it still needs knowledge of plant and animal taxonomy to be much higher and more widespread across the population than our specialised farming culture.

Wednesday, October 22, 2014

Botany picture #181: Cicendia quadrangularis


Cicendia quandrangularis (Gentianaceae), Australia, 2014. This tiny little gentian is an ephemeral weed introduced to Australia from the Americas. We saw it a few weeks ago at Mulligans Flat Nature Reserve. It is easily overlooked, but I had seen the other species of the genus before, and so I noticed it.

Monday, October 20, 2014

Botany picture #180, kind of: Populus alba

Just a few days ago my wife wondered about Floriade visitors who were so afraid of poplar (Populus alba, Salicaceae) seeds floating in the wind that they covered their faces while walking through. Yesterday she then discovered an article on the ABC website reporting that the seeds were wrongly blamed for hay fever which is, of course, in reality caused by pollen:
In parts of Canberra's inner south and the Australian National University's (ANU) campus the fluff can be so thick it looks like light snow.
But the head of Canberra pollen count at ANU, Simon Haberle, said the fluff was not actually springtime pollen.
"It is the seeds which are being blown around which you see and those seeds come in the form of fluff," he said.
"In reality it isn't pollen, so it is not associated with an allergic reaction."
This is news? This has to be said?

Not-pollen, as seen on my way to work today.

Now don't get me wrong. I am not trying to be the arrogant scientist here. In fact I would not expect the average non-botanist to actually know what pollen is. But here is the thing: the people who have hay fever? That is, the people who are allergic, and let me stress that, allergic against pollen?

Yes, those should kind of know what pollen is.

Still not pollen.

I mean, think about it. Imagine one of those hay fever-sufferers who are afraid of fluffy seeds meeting somebody who is allergic against bee stings but freaks out when they see a butterfly because they never bothered to find out what a bee looks like. They would see that as rather silly, right?

Or imagine them meeting somebody who is allergic against peanuts and then rejects an offer of lettuce because they think that is what peanuts are. Surely one would think them rather foolish for not learning the rather crucial detail of what precisely to avoid and what to consider safe. It is their allergy, after all; they should show some minimal level of interest, for the purpose of self-preservation if nothing else.

So why is it apparently considered perfectly normal for a pollen allergic to be entirely ignorant of what pollen actually is?

Those tiny yellow spots on my finger, however, are pollen grains.

(Also, why do people here, at least according to ABC, call a bog-standard poplar "the kapok or cotton tree"?)

Friday, October 17, 2014

Hotels, internets, and bridal industries

I have been in a hotel for a residential workshop the last few days, and one of the things that I really wonder about is internet service.

If you think about it, every kind of service gets better as go up the price range of hotels. I have stayed in cheap hovels in Bolivia where you had to bring your own towel, and towards the pricey end of the spectrum you will find shampoo supplied, television, fridge, etc.

Just about the only thing that gets worse with the hotel price is internet access. Your chances of having free internet are actually higher in a rural Argentinian backpacker hostel than in an expensive hotel in Sydney; in the latter expect to pay $5 per hour, Visa or Mastercard accepted.

Why is that so? When I raised the issue, people opined that the kind of person who stays at expensive hotels will surely not worry about $25 in internet usage. However, the same logic could be applied to everything else: the kind of person who stays at expensive hotels will surely not worry about paying $20 extra for a towel, yet no distinguished hotel would seriously consider failing to supply towels.

And before anyone argues that towels are a necessity but internet isn't, well, who can do without internet these days, especially businessmen or suchlike? I am still puzzled about the logic here.

------

The hotel has, by the way, won numerous awards from the Australian Bridal Industry Association (ABIA). This raises several other questions. What is a bridal industry? Why would anybody need a bridal industry? And if there is one, why is it a bridal as opposed to a wedding industry? Because that term carries with it the implication that the bride is expected to care about the wedding while the groom goes 'meh'. What century is this supposed to be again?

Friday, October 10, 2014

Limits to growth

Economics is not usually the topic of this blog, but this week I read something that I found quite remarkable.

Nobel Prize winning macro-economist Paul Krugman is usually a source of common sense, for example when he points out that an economic crisis in which businesses and consumers are unwilling to spend is probably not the ideal time for the government to also stop spending because then nobody moves money around and the whole economy just goes into tailspin.

However, he does appear to share the conviction of most economists that (a) growth is always desirable and (b) can go on forever. So earlier this week he reacted, with a piece entitled Slow Steaming and the Supposed Limits to Growth, to Mark Buchanan's admittedly provocative-sounding article Economists are Blind to the Limits of Growth by making the following argument:
After 2008, when oil prices rose sharply, shipping companies -- which send massive container ships on regular "pendulum routes", taking stuff (say) from Rotterdam to China and back again -- responded by reducing the speed of their ships. It turns out that steaming more slowly reduces fuel consumption more than proportionately to the reduction in speed: [...]

So what happens when you switch to slow steaming? Any one ship will carry less freight over the course of a year, because it can do fewer swings of the pendulum (although the number of trips won't fall as much as the reduction in speed, because the time spent loading and unloading doesn't change.) But you can still carry as much freight as before, simply by using more ships -- that is, by supplying more labor and capital. If you do that, output -- the number of tons shipped -- hasn't changed; but fuel consumption has fallen.

And of course by using still more ships, you can combine higher output with less fuel consumption. There is, despite what some people who think they're being sophisticated somehow believe, no reason at all that you can't produce more while using less energy. It's not a free lunch -- it requires more of other inputs -- but that's just ordinary economics. Energy is just an input like other inputs.
Or, to summarise his rebuttal: We can save some energy, and therefore there are no limits to growth.

Wednesday, October 8, 2014

Lunar eclipse today


Right now a total lunar eclipse can be observed in eastern Australia, and indeed perfectly from our front balcony. The moon has turned red, a phenomenon sometimes called a blood moon. The picture above was taken with my silly little digital camera, with about one second of exposure but at a high ISO setting.

Monday, October 6, 2014

Australia, land of dangerous animals


One thing that I noticed, and also discussed with another German couple yesterday, is that many Australians have an odd set of priorities when dealing with what one might call dangerous animals.

This is the continent of brown snakes, blue-ringed octopus, paralysis ticks, bull ants, redbacks, funnel-webs, box jellyfish, Irukandji jellyfish, stonefish, sharks and salties, and the Australians take it all in stride. Nobody seems to see a big problem with swimming in tropical waters or walking through the bush.

On the other hand, quite a few Australians seem to freak out when presented with the following - whoo! - daaaangerous animals: the honeybee and the European wasp. There are warning signs all over the place (see picture above), and yesterday I was told that the Australian National University has an actual "caution - bees in lavender" sign in front of one of the campus flowerbeds. The same person also told me of Australian friends who obsessively fumigate their patio whenever they see a single honeybee flying around.

Okay, so you can be allergic against their stings, but then again a brown snake bite can kill even non-allergic people. And many people become seriously allergic against bull ant stings, and those insects are everywhere, but nobody seems to mind.

Bees and wasps are really not that dangerous or aggressive; if we treated them like that in Europe we would have to have a warning sign every five meters and in everybody's garden. What is going on here? Is it just that they have been introduced relatively recently? But they would still have been introduced generations ago, right?

Saturday, October 4, 2014

Botany picture #179: Drosera peltata


Another one from our little walk last weekend: Drosera peltata. My five year old daughter finds carnivorous plants really interesting (who doesn't?). When she heard that there was a sun-dew, she rushed over and started explaining the way these plants capture their prey to our slightly surprised friends and colleagues, all three of them of course biologists themselves... but one of which had actually never seen a carnivorous plant in the wild before!

My daughter has her knowledge mostly from looking at and asking me to explain Adrian Slack's eponymous book which we have in an older German edition. Highly recommended, by the way.

Wednesday, October 1, 2014

Real and difficult problems

One argument that I have come across surprisingly often in recent times is this: Many smart people have thought hard about topic X and found it difficult, therefore X is a real and difficult problem. Examples would include the hard problem of consciousness and Gettier problems.

A closely related and likewise frequently heard claim is that some person Y's work and opinion must be taken seriously because they know a lot about a topic, have given serious thought to it, and published many books on it; in this case I remember the claim being made with reference to some theologian who Richard Dawkins had interviewed and whom he had supposedly treated very dismissively and arrogantly, but I have not seen the interview myself, so I cannot judge.

The problem is that while it may well be true that topic X is a real and difficult problem, or that person Y should be taken seriously, neither conclusion follows from this kind of argument.

Monday, September 29, 2014

Botany picture #178: Dianella


Today was a public holiday, and we met with some people to go for a walk in Mt Majura Nature Reserve. Among the spring flowers out was this Dianella (Phormiaceae); note the curly filaments and the morphological differentiation of apical and basal parts of the anthers. Unfortunately, figuring out what species it is seems to be rather hard in this genus...

Saturday, September 27, 2014

Botany picture #177: Klasea nudicaulis


Yesterday I finally received the specimens from my collecting in Europe earlier this year and started putting names on the so far unidentified specimens. The above species turned out to be among them: Klasea nudicaulis (a.k.a. Serratula nudicaulis, Asteraceae).

I can't help myself but the generic circumscriptions in the thistle tribe Cardueae don't really seem intuitive to me. I look at something like this and go, oh, obviously a Centaurea, and half the time it turns out to be something else, and I have no idea why. The characters used to differentiate the various genera in the keys are usually those that I would expect to be rather homoplasious, like the shape of the end of the involucral bracts.

Friday, September 26, 2014

Still don't understand what supernatural means

Some time ago I wrote that I don't really understand what supernatural is supposed to mean. Recently I took the opportunity of a discussion on whether humanism should or should not include a commitment to naturalism to pitch the question of what the opposite - supernaturalism - would entail. Although a few answers were helpfully provided, I sadly find none of them very useful.

Basically, I have the suspicion that although the word is continually used in rather important claims, such as that science has nothing to say about the supernatural, or that, see above discussion, one should not carelessly dismiss the supernatural, nobody actually has a clear definition of the concept supernatural.

Of course, a lot of people have examples that pop into their heads when they hear that word, and they would be tempted to reply with "something like demons and telekinesis". But that is not actually a definition, and my question is one step further back. Why would it be considered to be useful to call demons and telekinesis supernatural as opposed to natural? What is the difference between demons and horses, or between telekinesis and gravity, that would make it meaningful to call the first in these pairs supernatural and the second natural and, and this is where the important consequences come in, justify the conclusion that they are consequently beyond the scope of science?

To see what I am getting at, imagine that there is a thing or process called Ulkjam. You have never heard of it before, but I know all about it except whether it should be classified as natural or supernatural; that is what I want to know from you. You can ask me about all of its characteristics and attributes, and I will be able to answer. So what would your question(s) be to help you figure out as quickly and decisively as possible whether Ulkjam is supernatural or not?

So far, nothing useful has come up:

Monday, September 22, 2014

Botany picture #176: Romulea rosea


Some of the lawns in our suburb would look quite familiar to South Africans, I suspect, because there is an astonishing number of introduced plants from the Cape Region growing in them. In addition to the ubiquitous cape weed, which is really doing well for itself this year, there is also this little pink liliaceous monocot called Romulea rosea (Iridaceae). With its tiny size it seems harmless enough at first sight but it is apparently a declared noxious weed.

Another remarkable thing about it is the silliness of its common name: onion grass. Neither an onion nor a grass, this plant is thus a testament to the lack of imagination of its namers.

Thursday, September 18, 2014

Botany picture #175: Daviesia genistifolia


One of many local pea-flowered Fabaceae, this Daviesia genistifolia we recently saw at Mulligan's Flat Nature Reserve is not the kind of plant you want to accidentally fall into. The spines are quite unpleasant.

Tuesday, September 16, 2014

Phylogenetic trees in a matrix format in R

Yesterday, today and tomorrow I am participating in a workshop called 'Computational Macroevolution' run by Dan Rabosky, one of the leading experts in evolutionary modelling. Today we are learning about modelling changes in diversification rates, but yesterday he did a more general introduction into handling phylogenetic trees in R, especially with the APE package.

This was really useful because so far I have used R only for general statistics or plotting, never for dealing with trees. Among other things, it is interesting to see how R actually saves trees. It works like this:

In R, a phylogenetic tree is a list of four types of data.

The first is called Nnodes and is simply the number of internal nodes that the tree has. In a fully resolved tree, this should be number of terminals minus one.

Unsurprisingly, there is also a vector of terminal names.

The third element of the list are the internodes. They are organised as a vector of pairs of node numbers, where the first is always the parent node and the second is the daughter node. So a tree like ((A,B),(C,D)) would be structured as follows:

5 - 6
5 - 7
6 - 1
6 - 2
7 - 3
7 - 4

If there are N terminals, then nodes 1-N are the terminals themselves, obviously in the same order as in the vector of terminal names. Node number N+1 is always the root node, the others follow by order of distance from the root although really that is an arbitrary convention.

It is also obvious that a fully resolved and rooted tree will have two entries in the vector of internodes for every internal node. If there are polytomies then there are more than twice as many internodes as internal nodes, and there are less than N-1 internal nodes.

Finally, there is a fourth element of a phylogenetic tree, the vector of branch lengths (if any). The order is the same as in the vector of internodes.

I don't know exactly how an unrooted tree is handled but that will be easy to figure out. Anyway, useful stuff.

Saturday, September 13, 2014

Botany picture #174: Banksia serrata cone


A cone of Banksia serrata (Proteaceae), Australia, 2014. Often, seemingly simple and everyday things can lead to a number of intriguing questions when thought through. In this case, note first that there are very few follicles ("seed pods" - the red, hairy blobs in the picture) developing from what was a spike of dozens if not hundreds of flowers. In other words, most flowers were unsuccessful.

But why? Are these plants suffering from pollinator limitation, that is do they not get enough pollen to fertilise more flowers? Or do they get enough pollen, but most of it is from incompatible individuals? Many plants have incompatibility systems to ensure that they only accept pollen from sufficiently distantly related individuals, to avoid inbreeding. Maybe there just aren't enough compatible sex partners within a realistic distance, perhaps because the local population is genetically impoverished? Then again, maybe the plant could theoretically develop more genetically worthwhile fruits but it only ever "wants" to develop a few per cone because it cannot afford more, resource-wise, and so it aborts the rest. Offspring is expensive, and Proteaceae generally live on very nutrient-deficient soils.

Whatever it is, there is an interesting question here. I assume people will have studied it already, but I just don't know at the moment.

Another one is raised by the dry, dead flowers still attached to the cone. Some Banksias drop the dead flowers, e.g. B. integrifolia, some keep them. The latter state is often interpreted as an adaptation to frequent fire, but I recently heard an ecologist argue that many of the characters traditionally interpreted in that way arose before Australia dried out and became very fire-prone, so they couldn't have been adaptations. Well... don't characters always have to arise randomly before selection can begin to work on them? Where would you draw the line then?

That's the nice thing about the world around us: there is so much to figure out.

Wednesday, September 10, 2014

Multi-access keys, especially of the Lucid type

Long time no blog - I am somehow not finding the energy at the moment as often as I would like to. I would like to discuss a paper I recently found but before I can do that we need to lay some groundwork.

Previously I have discussed traditional dichotomous identification keys. They are the most familiar tool used for the identification of organisms, but there are less popular alternatives. Tabular keys are one option, and I have seen one a few years ago in a revision of the Bolivian species of a plant genus. It looked more or less like this:

Leaves <2 cm: P. vulgaris, P. aurantia, P. sericea
Leaves 2-5 cm: P. intermedia, P. reptans
Leaves >5 cm long: P. longifolia, P. boliviana, P. andina
Leaves glabrous: P. vulgaris, P. aurantia, P. andina
Leaves woolly: P. intermedia, P. reptans, P. longifolia
Leaves pilose: P. sericea, P. boliviana
...

Using a key like this is perhaps less intuitive and potentially a bit more confusing, but it can work quite well for relatively low species numbers. In the above case, for example, you would know immediately that you were dealing with P. andina if your sample had glabrous leaves longer than 5 cm because that species is the only one with that specific combination of characters. On the other hand, if you had very small glabrous leaves on your specimen it could still be either P. vulgaris or P. aurantia, so you should look for additional characters further down the list.

But as mentioned, this quickly becomes unrealistic for larger numbers of taxa; you wouldn't want to navigate such a table if every line listed more than twenty species possessing that particular character. Luckily, these days we have computers to help us with managing the data, and this is why tabular keys are becoming more popular.

The way this works in practice is that the taxonomist who wants to build a key produces a character-by-species table which the end user will not have to deal with. Instead, the end user is confronted with a software tool that allows them to enter whatever characters they can easily see, and each time they enter one the program throws out all the species that do not match the new information. The identification process ends when the possible species have been narrowed down to one or, more realistically a small number that the user may then check individually to see if one of them looks like the specimen they have on hand.

Perhaps the most popular software tool for building and displaying digital multi-access keys is Lucid, which, however, is not open source. Example identification keys for various groups can be found on their key server. The one that I am most familiar with is the Wattle Key to the Australian species of Acacia (Fabaceae). The screenshots below are accordingly taken from the Wattle Key, merely to demonstrate how Lucid Keys work:


There are four windows. The upper left one shows characters, the upper right one shows all the species, in this case 1274. The lower two windows are empty at the beginning. Now if we enter a few characters...


...we see that the characters that have been used appear in the lower left window. On the right, excluded species have moved to the lower right window while the ones that are still matching the available information are still in the upper right one. Our goal is to get their number down as far as possible.

The trick here is obviously to know which characters are more likely to be useful. In the present case, I pretended to have a bipinnate Acacia in front of me simply because I know that there are relatively few of them. Eh voila, as we see my two character selections already excluded all but 50 species.

This looks pretty straightforward, but of course if you don't know the plant group that well you won't know which characters might be important. In that regard a dichotomous key is more helpful because here the specialist who wrote it will have selected the most important characters for the first few questions of the key (if they are competent, that is). On the other hand, if you don't have the characters on your specimen that the first two questions of a dichotomous key ask for, for example because they are fruit characters but your specimen was still only in flower, then you are better served with a multi-access key.

When I next post about identification keys, some more of the pros and cons of both approaches will become obvious.

Friday, September 5, 2014

Botany picture #173: Cassytha glabella


A genus that I had never heard of before I came to Australia is Cassytha. As a twining, fully parasitic plant that has lost leaves and roots, it represents a remarkable case of convergent evolution with the dodder genus Cuscuta. Whereas the former is a member of the Lauraceae and as such of a very early diverging ("basal") lineage of flowering plants, the latter is deeply nested within the Asterid clade of the Eudicots. Shown here is fruiting Cassytha glabella, observed at Jervis Bay a few days ago. It appears to be parasitising on a member of the heath family Ericaceae.

Tuesday, September 2, 2014

Consciousness and the Fallacy of Composition

I wrote some time ago that I consider the Just World Fallacy to be perhaps the most pernicious fallacy there is, but lately it seems as if the Fallacy of Composition is popping up in discussions everywhere. Its influence is certainly not as destructive socially and politically, but it seems awfully widespread, and it seem to easily confound the thinking of otherwise smart and reasonable people.

What is the Fallacy of Composition? It is the mistake of concluding that the whole must have some property that its parts have individually or, perhaps more relevantly for present purposes, that the whole cannot have any properties beyond those of its parts. For example, one would be mistaken to conclude that birds cannot fly from the fact that individual feathers or leg bones are incapable of powered flight. So far, so obvious.

Where I increasingly notice the effect of this fallacy is in discussions of mind, consciousness and artificial intelligence. The funny thing about it is that the same mistake appears to be made by people on the most extreme ends of the spectrum, that is mind-body dualists and religious believers on one side and straight-laced rationalists and physicalists on the other side.

Monday, September 1, 2014

Waterfalls, this time with actual falling water

A few weeks ago I went to Jervis Bay with ANU lecturers and students for the third time. I always wanted to show the area to my family, and this weekend we finally managed to go camping there. My wife enjoyed the native plants and animals, my daughter loved the beach, and both admired the landscape.


On the way there, we stopped at Fitzroy Falls in the Moss Vale area. This impressive waterfall is 81 m deep, but as can be seen in the above picture there was quite a lot of fog so we could not see it under ideal conditions. This place is really wet most of the time, the vegetation is pretty much a temperate rainforest.


On the way back, we also stopped at the same place as I did with the student field trip - Tianjara Falls. Then I called it an alleged waterfall because it was dry, but this time we were rewarded with a much nicer view! For some time there was even a rainbow in the spray.


To end on a somewhat weirder note: The family posing in front of the Big Merino of Goulburn. These various big whatevers of Australia are of course greatly amusing to a five year old, but I wonder what archaeologists of the future are going to make of a megalithic sheep. If it can still be reconstructed after two thousand years it will probably be assigned some kind of religious significance. Then again, I doubt that a structure like this one will last as long as Roman masonry.

Thursday, August 28, 2014

Botany picture #172: Acacia decurrens


I am reasonably optimistic that this is indeed Acacia decurrens (Fabaceae), one of many wattles that are currently in flower here in Canberra. This was a small tree in Mount Majura Nature Reserve. It is the first time that I notice an Acacia with the styles of the individual flowers sticking out of the heads like that.

Wednesday, August 27, 2014

Final update on using fastStructure and similar software

After my somewhat mixed experience trying to use fastStructure, I have recently found the time to throw my data at two other programs for inferring population structure.

To recap, I have thousands of SNPs for two groups of species, in one case from 91 individuals and in the other from 224 individuals and I want to know how best to group the individuals into separate 'populations', in the present case potential species. I originally used fastStructure because it was new and supposedly written specifically for large numbers of SNPs, but the results were ultimately odd. The clusters didn't make very much sense and the program found virtually no admixed individuals, that is hybrids, although there really should have been some.

Earlier this week I then tried the R package adegenet. On the plus side, it turned out to be very simple and user-friendly. Of course you need to know how to use R, but the manual of the package is well written, and adegenet has a straightforward "read" function for importing datasets. It easily imported my Structure file without any hiccups, and after that it was a simple manner of handing my data over to adegenet's "find.clusters" function.

However, I tried different settings and did not get reasonable populations with any of them. One problem in my dataset are missing data, and I found that setting allele frequencies to zero for those cases produced the most meaningful results, but still there were several populations with no samples in them and the populations that had samples didn't make a lot of sense.

Yesterday I finally tried my luck with good old Structure itself - somewhat hesitatingly because I feared it would be very slow with such a big dataset. Yes, even for my smaller dataset what I wanted to do ran overnight, but that is still faster than I feared, and the results are worth it. The populations make sense, and in marked contrast to fastStructure it finds evidence of admixture. My larger dataset will probably need several days to be analysed, but if that is necessary so be it.

There is probably a reason why that program is the most popular in the area...

A new low in science spam

Science spammers sometimes use scripts to mine journals or article databases for authors' contact details and then generate automatic spam. That saves them a lot of work, of course, but one has to wonder about the efficiency of that approach because the results are so bizarre and off-putting.

Behold:
Dear [my name]; [name of co-author]; [name of co-author]; [name of co-author]; [name of co-author]; [name of senior author],
Once you published a paper titled [name of our paper] in [name of the journal] . With such attractive theme [what follows are the keywords of our article] Cell size; chromosome; flow cytometry; genome size; guard cell size; ploidy, the article is so outstanding. It shows your professional and rigorous attitude. On behalf of the academic world, we appreciate your contribution to the research filed [sic!] very much. And we wonder if you have any new progress or you are doing any new study about your interested field.
Science Publishing Group [link], who [sic!] publishes Journals, Special Issues, Books and Conference Proceedings, now sincerely invites you to contribute your new articles to the website.
[another link]
Submit Your Latest Research
New progress of your latest research
New study in your research field
A view for the new research trends
Please submit your new papers via:  [another link]
Advantages to Publish with SciencePG
Peer Review: Effective and professional
High Visibility: Up to 40,000 visitors per day
Open Access: Open to the public free of charge
Low APC: Article Processing Charge ranges from 70 to 270USD
Abstracting and Indexing: WorldCat, CrossRef, JournalSeek, CASSI, etc.
If you are doing some new study, please kindly notify us. And we are looking forward to your participation.
It is even worse because all the fields that were filled in by the script are in italics in the original (like the keywords above), making it even easier to see what is going on. So sad.