Saturday, November 11, 2017

What race is a dickhead, indeed

Reading the recent news items about an Australian senator with Muslim background being abused in a pub by a bunch of racists, two thoughts occur to me. The first regards the oh so clever comeback by one of those racists after being called a racist: "what race is Muslim?"

The thing is, of course, that there are legitimate and illegitimate cases of people being called racist. If, for example, a hypothetical atheist were to say, "mainstream Islam as currently practised is problematic to me because so many of its adherents consider homophobia and sexism central to their beliefs and identity" then calling that statement racist is just wrong. Maybe that atheist is also mistaken, and maybe they are also incidentally racist, but the argument as stated would be explicitly about a belief or behaviour, regardless of what particular person holds the belief or shows the behaviour. It is not a racist statement.

This present case, however, isn't that. Somebody who says, "why don't you go back to Iran" and calls their opposite "monkey" is clearly not making an argument about theology; they are just being racist. Those statements are what is called a dead giveaway.

The second thought is the same that I always have when reading about white racism in countries like the USA or Australia: I gawk, open-mouthed in amazement, at somebody whose ancestors lived in Europe a mere two hundred years ago telling somebody else to "go back" to the country of their parents. Ye gods, one of those guys apparently called himself an "original Australian". The mind boggles. One wonders which Aboriginal tribe he identifies with, and what the other members of the tribe think about that...

Tuesday, October 24, 2017

Botany picture #254: Trifolium glomeratum

Trifolium glomeratum (Fabaceae), seen today at Mount Majura Nature Reserve. Admittedly if one asked me for the prettiest clover species this one would not even make the top fifty...

Dragonriders of Pern

Having now read the first volume of Anne McCaffrey's Dragonriders of Pern, an apparently wildly popular kind of science fiction-y series, I am somewhat puzzled why it is so popular and glad I did not buy more than two of them. Spoilers ahead, although given that I have so far only read the first of what are, according to Wikipedia, at least 23 novels, I probably still know very few of those.


My first thought is actually: this is a bodice ripper novel with dragons. The main male character, a guy with the unfortunate name F'lar, is kind of an abusive dick; the narration seems to consider it not only okay but even charming that he cannot properly express his feelings for his love interest (see next paragraph) except by violently shaking her whenever she did not do what he wanted. What is more, even in his own thoughts he describes their first sex as borderline rape. The only thing missing is a cover image of a "scantily clad woman being grabbed by the hero", to quote a relevant Wikipedia page.

The main female character, Lessa, shows nearly all key traits of a Mary Sue, at least in my eyes. She is unusually beautiful, of very noble blood, a singularly gifted telepath, and of course she bonds with the most impressive dragon ever, an unusually large and fertile golden queen dragon. She had a tragic youth but does not appear at all traumatised. The men admire her and other young women are jealous of her. (Also, other women who aren't her friends are generally depicted as sluts.) Everything she does, no matter how stupid at first sight, ultimately turns out to have been exactly the right thing to do.

Really one gets quite fed up with both F'lar and Lessa at some points.

The world

Pern is a planet that was in the distant past colonised by humans. Every 200 or 250 years a rogue planet called the Red Star comes close enough to Pern for c. fifty years to throw down spores called Thread. This Thread voraciously consumes all organic matter. The ancient Pernese reacted by genetically engineering local wildlife into fire breathing, flying dragons and bonding them to telepathically gifted humans, who form the top tier of a rigidly feudal society. Together, these teams of dragon and rider rise up in large squadrons and burn the Thread out of the sky while it is falling. Also, the dragons can teleport (!) and, under special circumstances, jump through time.

The need to bond dragons to humans is well justified in that the dragons are fairly short-sighted and impulsive without human guidance, showing for example a tendency to gorge on food. And unfortunately the early settlers soon lost their space age technology, what with having a very small starting population and a metal-poor planet, so that solving a technological challenge by leaving your descendants GMO animals seems like a good plan.

The funny thing is, and here it probably just shows that I am a biologist, that I can easily take the teleporting and fire breathing in stride but am rather bugged by the biology.

First, the Thread. How the hell does that even start to make sense? Maybe later books offer a better explanation, but Thread eats organic matter so voraciously as to be physiologically impossible; it is more like concentrated acid than like a living, growing organism. What is more, it eats and grows so quickly that it soon consumes everything and dies in turn. This is just not how life works, and the word parasite, although used explicitly by F'lar, is completely misapplied, as a parasite would be stupid to kill its host so quickly. And how does the Thread persist for thousands of years on the Red Star if it is so voracious? What does it eat there? It just does not make sense.

Next, the dragons. Again, teleporting, physically impossible but no serious hurdle for my willing suspension of disbelief. Fine. Fire breathing, ditto. The main time travel gimmick of the story, it has to be said, is actually really stupid, both because it is caused by itself and because the narrative puzzle that it solves is introduced just a few pages before. (Seriously, this should have been developed in the first quarter of the book, feeding the reader little clues here and there over the next chapters, but no... Imagine a crime mystery novel where the murderer gets introduced for the first time on page 209 and then convicted on page 211 and you get an idea of how this felt.)

But what really bugs me about the dragons is their reproductive biology. There are five colour groups:
  • the very rare golden queen dragons, which are female and fertile, and whose female riders automatically become the boss women in dragonrider society;
  • the relatively rare bronze dragons, which are male and fertile, and whose male riders have high status (the riders of the bronzes who mate with queens get to be the boss men in dragonrider society);
  • brown dragons, male and sterile, bonded to male humans;
  • blue dragons, male and sterile, bonded to male humans;
  • green dragons, female and sterile, weirdly also bonded to male humans.
Now the obvious question is, why the heck would there be any but the first two classes? Males, females, done, the rest could just as well be called "pointless dragons". And why do there have to be queens in the first place -- just because social insects are cool? Well, if that is the point then at least have golden female, bronze male, and brown sterile worker dragons, that would make marginally more sense except that top level predators do not really need a worker class.

Finally, at the time of the first novel the dragonriders have just spent 400 years reduced to a single dragon nest, with only a single queen at each given moment in time, so that she would always have had to mate with her brothers. Realistically the inbreeding would have been lethal, but instead it turns out (at the beginning of the second book) that those 400 years have made the dragons larger and more fertile than before! You fail genetics forever.

But okay, maybe others will dismiss the genetics, reproductive biology and physiology issues just as I dismiss the physical ones. The main problem is still that the book was actually not very well written. I had read Jonathan Strange and Mr Norrell just before the first Pern novel, and I am sorry to say the difference was striking.

Monday, October 16, 2017

What works and what does not work in contemporary science?

Today I participated in a workshop on the way forward for taxonomy in Australasia, so it might be a good opportunity to come back to the topic of the bioinformatician who thinks that all of science is broken and to consider what works and what does not work, at least in my view, in the field of science that I have the most direct insights into. I am not limiting myself only to taxonomy but will include all the broader field of systematics, but taxonomy is a major component.

Funding: Everybody says that funding in their field is too low, so this applies across all of science. But are scientists just whining? No, I believe that there is indeed too little competitive research funding available.

First, I have seen and heard of lots of cases where funding agencies have to reject very valuable proposals because there simply isn't enough money to fund everything that would be good to fund (sometimes apparently called 'approved but not funded'). Second, there are many funding agencies where you have success rates on the order of 2-10%. So to conclude that funding levels for competitive grants are high enough we would have to believe that 90-98% of applications are useless and that the weeks that the unsuccessful applicants have each invested into writing their many applications could not have been used in a more productive way. And that seems like a big ask.

Incentive structure: This is the big one, at least to me, and I guess here I find the most overlap with the aforementioned frustrated bioinformatician. What basically happens is that people are rewarded with jobs and promotions for (a) having publications in JCR-listed journals, in particular if those publications are cited a lot by other papers in other such journals, and for (b) getting external research grants, but of course the decision whether somebody gets a grant is also partly and sometimes mostly based on criterion (a). This is simplifying a bit, as there are also, depending on the job, teaching, textbook writing, conference participation, etc., but not by much. Publication lists are usually the key factor.

The problem is not that publications are a key factor though, because if a scientist does not publish their research it is indeed wasted. The problem is that there are lots of useful outputs that scientists can produce that are not, very specifically, research papers in JCR-listed journals.

Perhaps the most impactful thing a taxonomist can do for end users is to produce a publicly accessible online identification key or to contribute to a flora. But no matter how often this output is used to identify organisms, how many people need it for their work, it does not count the tiniest blip towards the taxonomist's number of citations or their h-index. There is no requirement for the end-user to cite a key in a paper, even if they used it during their work; and even if people cited it, it wouldn't count because an online key or flora volume is not captured by the JCR. Consequently, in terms of career advancement the taxonomist would have wasted their time and should instead have produced journal articles cited by other journal articles.

It is clear that people largely do what is rewarded, and largely cease doing what is not rewarded. So to the degree that there are useful things for scientists to do that do not result in publications in JCR-listed journals the incentive structure in science leaves something to be desired.

More generally, I feel that there is too much of a focus on flashy results and innovative methods but too little appreciation of incremental, everyday work. One of the surer ways to be cited a lot appears to be to develop a new lab method or a new piece of analysis software. This visibly leads to conferences full of rising stars each promoting their own new Bayesian analysis method or bioinformatics pipeline, but very few early career researchers contributing to specimen identifications, describing new species, or conducting taxonomic revisions.

Now to publishing itself. Apart from what I wrote in the previous section, in terms of academic papers I am actually not all that unhappy with the situation. Yes, ideally one would have all journals run as public utilities, cost-free to publish in and cost-free to read, instead of having private quasi-monopolies with massive profit rates and, pick your poison, either research locked away behind paywalls or money that could go towards research spent on publication fees.

But in a system where somebody has to pay I prefer subscription-based funding instead of author-pays open access, which is promoted by many people frustrated with the status quo, because in the latter system the incentives are perverse: journals are financially rewarded by accepting as many papers as they can instead of maximising the quality of their content.

As for peer review, again the system as currently implemented seems to work reasonably well; that is why it evolved to be like it is in the first place! I have received good feedback in many cases. I also had one or two cases where I believe the manuscript was unjustly ripped apart by an individual reviewer, but well, there are human egos involved, and one should not make the perfect the enemy of the good. I am trying to be a charitable and constructive reviewer myself but also suggest rejection papers where the conclusions do not follow from the results or where the methodology cannot address the research question.

If there is anything that I see as a current problem it is that there are rumours of journals increasingly being unable to find enough reviewers, which suggests either a lot of free-loading going on or journals being too unimaginative with reviewer invitations, or both. (Certainly I do not appear to get as many invitations from mid-level plant systematics journals as I would expect if they are struggling to find referees.)

Reproducibility: As I wrote in the previous post on this issue, I do not see any evidence whatsoever that taxonomy, phylogenetics, systematics or evolutionary biology have a reproducibility problem.

So that is how I at least perceive that part of science that I can judge best, for what it is worth. More money would be good, but an even more intractable problem is that the incentive structure currently in place does not reward some of the most useful and impactful work that systematists could be doing. Note that neither of these problems would really be solved by scrapping journals and publishing everything on preprint servers, but more on this maybe in another post.

Everything is about white male privilege, even writing advice it seems

I read a headline saying Why the writing advice 'show, don't tell' is inherently political and thought, well, this should be good. The links ultimately lead to an essay called Let me tell you by one Cecilia Tan.

The author discusses 'show, don't tell' (SdT) entirely in the context of world building, i.e. info dumps about the background of a story. She then argues that SdT relies on a shared cultural background, and thus this writing advice privileges writers who can rely on sharing such a background with their readers, i.e. white males.

Now, first, I would not see anything particularly wrong with this in principle, because why should it only apply to white males? If an Iranian woman wrote a novel for Iranian women, it would work the same.

But more importantly, at least to me, and while I appreciate that I am not an author of novels who has run into that criticism myself, her understanding of SdT totally misses the point. Every single time I have seen people complain about being told instead of being shown by a poor writer it was something like this (if necessary search that page for "show-don't" to find what I mean) or this.

So it is not about world building info dumps at all. It is entirely about being too poor a writer to communicate the abilities and emotions of one's characters. It is about merely stating that your protagonist is a good debater instead of introducing her by winning an argument. It is about thinking that your reader is too stupid to understand that the protagonist is sad when you simply write "Frodo cried" and instead writing something to the effect of "Frodo cried because he was sad, and he was sad because as you may not remember Gandalf had just fallen to his death, see previous page". It is quite simply about poor and lazy writing, in a way that is independent of cultural context except to the degree that some other cultures may not even have a tradition of fiction writing (e.g. if it is a culture without a written language).

But apparently everything has to be about Western privilege all the time; there is nothing in the universe that is not about Western privilege.
It's the same hubris that led the white Western establishment to assume its medicine, science, and values superior to all other cultures. We'll come back to that shortly.
Eh, no. A medicine is superior to other medicines if it heals more reliably, and a scientific methodology is superior to other scientific methodologies if it produces more reproducible and accurate descriptions of reality. There are things that demonstrably work (often including substances found in traditional healing herbs) and there are things that demonstrably don't (including the Western tradition of bloodletting). That is all there is to it, no Western or Eastern or whatever needed.

Also, apparently a story about a protagonist having an impact on the outside world is quite simply "colonialism". What? No, people interacting with each other, helping each other against a dark lord's attempt at world conquest, learning from each other isn't colonialism. Invading with an army and taking over other people's countries to exploit them, that is colonialism. Words have meanings. Or at least they should.

Sunday, October 15, 2017

Monga National Park

Monga National Park is c. one and a half hours east of Canberra along Kings Highway. It features wet sklerophyll / rainforest type habitats with many cryptogams.

We were there today in the hope of seeing Telopea mongaensis (Proteaceae) in flower. As can be seen in the above picture we were still a bit too early in the season, they are only just in bud. So far I have seen the Tasmanian species T. truncata, the New South Wales State Flower T. speciosissima, and, during a holiday in Victoria and southern New South Wales, T. oreades. The latter appears to be very similar and, I presume, most closely related to T. mongaensis.

What was in flower a lot in the same locality (the Waratah Walk from Mongarlowe River Picknick area) was Tasmannia lanceolata (Winteraceae), member of a 'basal' angiosperm clade, but of course it is far less spectacular.

This is the habitat; Telopea mongaensis is found particularly along the river.

The other attraction just a few hundred meters away is Penance Grove, which we had seen before. It is particularly known for its many tree ferns.

I am always fascinated by Dawsonia superba (Polytrichaceae), the largest moss in the world, which I believe is most easily accessed from Canberra by coming to Monga NP. I have written about it at least twice before, but I think this was the first time I saw it with young sporangia.

Tuesday, October 10, 2017

The world is so confusing sometimes

When will we finally reach peak gibberish in science spam?
Dear Author,
Formatting as in original - an auspicious start.
Journal of Proteomics & Bioinformatics greets you a good day!!!!
That's a new one, but at least it isn't "greetings of the day". Also, by the way, I really don't understand why my spam filter cannot finally figure out that anything that has more than one exclamation mark in a row can be binned immediately.
We are in shortfall of articles for successful release of Volume 10, Issue 10.
See this circle? That is my circle of caring. The fact that this alleged journal cannot fill its issue is about 5,000 kilometers outside of my circle of caring. So...
Is it possible for you to support us with your transcript for this issue before 30th October?
What do they mean with "transcript", which is usually a sheet showing university marks (grades)? Do they not even know the word manuscript?
If this is a short notice please do send 3-4 pages Short Commentary or Mini Review, and hope that a 5 pages article will not take much time for an eminent like you.
What does this sentence even mean? Help?
Also it will be very kind of you if you can acknowledge the receipt of this email and give your opinion to our proposal.
Better not, because if I honestly gave my opinion of their proposal there would have to be some bad language involved.
Best wishes,
Susan Williams
As usual, if this was written by somebody actually called Susan Williams... oh, excuse me, Susan Williams, then I will not only eat my hat but a whole stack of hats.


In completely unrelated news, why does GBIF suddenly use hexagons?

This looks as if somebody tries to draw in more people who enjoy strategy computer games, but it seems a bit odd given that spatial studies generally use square grid cells, either equal area or degree-based.

Saturday, October 7, 2017

No, science is not fundamentally broken just because one person had problems with their supervisor and prefers preprint servers

While on holidays I learned about an interesting case in food science, where it is suspected (at least according to some statisticians who have dived into the literature) that a very prominent researcher may have P-hacked, self-plagiarised, potentially reused the same dataset for several publications while making it appear as if they represented independent studies, and used self-citations to support statements that they don't. I find stories like those at the same time interesting, inspiring and very, very frustrating.

Interesting because, well, human nature and all that, and I am continually puzzled whether the people in question really think it won't come out in the end. Inspiring because this is how science self-corrects; not necessarily by individual scientists changing their minds (although that would be the ideal), but by open debate between scientists and careful re-examination of data. And frustrating because of exaggeration, over-generalisation, and naiveté about the solutions or alternatives to the problems that are identified. This post will mostly be about over-generalisation as found in the writings of one Jordan Anaya on Medium.

He evaluates and criticises the relevant food scientist's working practices, as do many others. But in doing so, he writes the following:
But I am interested in how academia selects for bad science, is free from any outside regulations that might prevent a crisis like the housing bubble, and how its power structure allows senior members to behave like dictators.
Science in academia is not about performing science, it is about your brand.
We are in the midst of a reproduciblity crisis in science,
all the problems science is currently facing
As it stands now, the wrong papers get published, the wrong researchers get funded. There is no incentive to share data or perform careful science. The only thing that matters is your brand, and your ability to leverage that brand into publications and grants, which circle back to feed the brand. If that means performing sloppy research, exaggerating results, and then refusing to acknowledge any errors, so be it.
Most of the literature is wrong, this is just a reminder that we need to be vigilant. It is also your daily reminder that peer review is useless and everyone should instead be preprinting their work.
I find this nothing short of astounding. Here is a bioinformatician generalising from his own bad experience in what appears to be one research group and one case in food science across all of academia and across all of scientific research. He does not write, "food science seems to have a problem", no, it is all of science, based on n=2.

When he writes that academia selects for bad science, can he really say with confidence that that is the case for, say, Australian entomologists? How would he know?

When he writes that it has no outside regulations, does he really mean to claim that it is not ultimately voters who decide through elected governments what kind of research will get funded? Is there so much money in cancer research in spite of or because of the wishes of the public? And this is before mentioning industry collaborations and industry-funded grants. (I will grant him that science isn't a democracy. The question is whether it could work as one, but that is beyond the scope of this post.)

When he writes that science as currently practiced in universities is not about science but about branding, can he know that this is the case for inorganic chemistry in southern Germany?

Do astronomy and phylogenetics really face a reproducibility crisis? I at least am not aware of that, and indeed I would be confident that if somebody were to repeat pretty much any phylogenetic study published in a serious journal with different molecular markers they would be able to reproduce all major results.

Is surface physics really facing "all the problems" that food science does? Again, how could Anaya even pretend to know?

How does he know that the wrong papers get published and the wrong researchers get funded in, say, plant ecology or archaeology? He claims that there is no incentive to share data - has he never heard of GBIF, Genbank, TreeBase or Dryad, or of all the journals that will not even accept your paper if you haven't deposited your data in a publicly available repository?

"Most of the literature is wrong." Seriously? Meaning I could pick a random article from a well-respected taxonomic, systematics or evolutionary biology journal and there would be a more than 50% chance that it is "wrong"? (And what qualifies as "wrong"? Does it mean this group of plants dispersed to Australia 16 million years ago instead of the currently accepted 15, or does it mean evolution is a lie meant to destroy Christianity?) And the alternative is to do away with all quality control whatsoever? But I am getting ahead of myself, this post is meant to be about over-generalisation, not solutions.

There is no doubt that the way science is being practiced leaves room for improvement, in particular in the areas of research funding, incentive structures, publishing, and recruitment. Okay, the same is probably true for any collaborative enterprise that humans have ever undertaken or will ever undertake, but tu quoque arguments don't change the fact that a lot can be criticised. I would have quite a few ideas for improvement myself.

Still, I hope one thing is clear: the fact that there are problems and some people acting in bad faith does not mean that an entire enterprise is broken. When we find that there are incentives for teachers to inflate grades we do not conclude that all of education is broken; when we find a certain percentage of police officers are racists we do not conclude that all criminals should go unpunished. And you may have heard that when we pour out the bathwater we usually take care not to pour the baby out with it.

Of course it is a question to be debated whether the entire system is broken. It could be. But from what I can see in plant systematics, ecology and related fields, this is so much hyperbole. In fact I am struggling to find a description of the act of dismissing all of science and the careful work of thousands of researchers with a mere "most of the literature is wrong" that is reasonably polite and does not involve phrases like "breath-taking arrogance".

It is also, of course, ridiculously irresponsible. Think of anti-vaccinationists, creationists, climate change denialists, alternative history cranks, expanding earthers, and any other set of conspiracy theorists. They already claim that science is all broken and the literature can't be trusted. Now they can say that a scientist frustrated with the review process in his field confirms it. Believe what you want, because the scientists can't be trusted!

Ye gods. Did the plain truth - science publishing and funding have serious issues that we need to tackle, and there are a few frauds just like in every other profession, but all in all we can trust most of our colleagues to be well-meaning and most of the literature to be useful - not sound sensationalist enough?

Sunday, October 1, 2017

Spring holidays 2017, final part 5

And we are back. Today we returned to Canberra passing through, among other things, the Putty Road between Wollemi and Yengo National Parks. It is a very nice, forested landscape, although it would be even better if there were one or two official lookouts in the southern part.

The above gives an impression of the road as seen from a little resting area along the way, in this case still very much towards the northern end.

About 40% or so of the way towards the south there is a locality called half-way house that was apparently once a cafe and petrol station. Now there is only a stall that sells coffee, soft drinks and snacks as well as metal and wood sculptures, thus the large statue above. I got a coffee.

Slightly before that spot we saw Conospermum taxifolium (Proteaceae) along the way. Their flowers are a bit different from the 'usual' Proteaceae that people are familiar with, such as Banksia or Grevillea. In Western Australia this genus is a striking part of the landscape in the form of the smoke-bushes, but the species here in New South Wales are less conspicuous.

Because this post does not have enough plants yet I am returning to one we saw at the beginning of the trip. It is among numerous photos that I did not upload because I was uncertain about the identification, but now I am reasonably optimistic that this is Darwinia procera (Myrtaceae), a rare and very localised species.

Thursday, September 28, 2017

Spring holidays 2017, part 4

Yesterday and today we continued to explore Myall Lakes National Park and its surroundings.

The village of Hawks Nest is very touristic, and so it is perhaps not a surprise that it has a spring flower walk that is recommended to tourists. And indeed there are masses of flannel flowers, but also other interesting plants.

At the other end of the National Park we today visited the lighthouse at Sugarloaf Point. Shown here is the view towards Seal Rocks, which unfortunately wrecked many ships even after the lighthouse was built, apparently due to prevailing wind conditions during one part of the year.

Botanically today's topic is climbers. Our first one is Kennedia rubicunda (Fabaceae), with surprisingly large red flowers.

I am reasonably certain that this would have to be Geitonoplesium cymosum (Smilaceae), a climbing monocot. The field guide calls it 'scrambling lily'.

Finally, the native passionflower Passiflora herbertiana (Passifloraceae) had been teasing us for a few days now, always there but never in flower. Today we finally found it in bloom, and that made my day!

Oops. Upon examination of the Flora of NSW key to Passiflora it turns out that this is introduced Passiflora subpeltata from Brazil, as it has large, leafy stipules. Also the Flora says that native P. herbertiana is red, which is really interesting because Fairley & Moore's Native Plants of the Sydney Region, which serves as my quick reference in the field during this trip, shows it as white.

Either way the one we saw is not native. Still, passionflowers are just something else, and they remind me of past field work in the Andes.

Tuesday, September 26, 2017

Spring holidays 2017, part 3

We spent half the day at the beach and then the rest exploring Myall Lakes National Park. We saw lots of plants, but as I haven't had the time to check many identifications I will only post two. They are nice ones though:

Actinotus helianthi (Apiaceae) is the famous flannel-flower. The petaloid bracts around the flower-heads are felt-like, thus the English name. Many people wrongly believe it to be a member of the daisy family, but it belongs to the family of parsley and fennel.

The second one makes me very happy indeed. I had heard of the flying duck orchid (Caleana major, Orchidaceae) and seen photos, but now I have seen it in the flesh, as it were. Surely one of the weirdest-looking orchids on a continent that has many weird-looking ones.

Monday, September 25, 2017

Spring holidays 2017, part 2

Well look at that, holiday parks have free Wifi now...

Today we arrived at the place where we planned to pitch our tent, Hawks Nest just at the south end of Myall Lakes National Park. On the way we spent a bit of time in Brisbane Water National Park, which of course is nowhere near Brisbane but instead just out of Sydney.

But first we had to get out of Sydney, and here it seems to me that the road engineers there might want to look into the concept of a city highway that moves travelers through the area with a minimum amount of fuss. Think a straight road with a turn-off every few kilometers instead of a winding nightmare leading right past houses and shops and interrupted by traffic lights every few meters.

Ah well, think of the flowers.

The first decent stop out of Sydney was at Moonie Moonie Creek, which I think actually deserves a promotion to "river" here.

And our last longer stop was at Girrakool, a resting area with several great walks. This photo above shows a place where one can get down to the pools and creeks, but there are also lookouts across the valley and longer loop walks.

Now for the plants. Myoporum acuminatum (Scrophulariaceae maybe? It changes), a shrub at the edge of a swamp near Moonie Moonie Creek.

There were lots of interesting plants on the shallower soils at Girrakool. Here what I take to be Kunzea capitata (Myrtaceae). It is not the plant's fault that it reminds me of Otto Kuntze, but unfortunately it does.

Right next to it we saw Grevillea speciosa (Proteaceae). There are of course lots of Proteaceae here, but there are few where I am as sure about the identification as with these characteristic leaves.

Finally, Mirbelia rubiifolia (Fabaceae), a very cute little pea-flowered legume.

Sunday, September 24, 2017

Spring holidays 2017, part 1

Family camping trip over the spring school holidays! Having previously camped in what is parochially called the "South Coast" (in New South Wales Sydney is the navel of the world, so it does not matter that the coast is on the east of the landmass) and visited the New England area further north we decided to go for the area just north of Sydney this time.

Today, however, we only made it as far as the south of Sydney, taking it slow and seeing things on the way. The main attraction here is Royal National Park, which my wife had seen fifteen years ago but my daughter and I have now seen for the first time.

The above is the view from Bald Hill lookout, as we were coming into Royal National Park from the south, via Wollongong.

We also saw some tall sklerophyll forests, but like most of south-eastern Australia this area has seen too little rain this year, and much of the vegetation was too dry. The heath looked much better. This species is Isopogon anemonifolius (Proteaceae).

Another Proteaceae, we think it is probably Grevillea oleoides given its very long and slender flowers and likewise long and slender leaves.

Again we are not entirely sure, but this may be Lasiopetalum parvifolium (Sterculiaceae); the field guide is not entirely clear but it looks as if the other species of that genus that are in the area and have similar leaves may differ in having hairs also on the inside of the sepals. It is a small shrub that I photographed in a very dark spot using the tripod.

And this is where we got out of Royal National Park, Bungoona lookout at its northern end.

As we are going camping I will presumably not be able to post anything else until Friday at the earliest, but then I hope to be able to upload a bunch more plant and landscape photographs.

Friday, September 22, 2017

Three plants near Wollongong

After a work meeting in Wollongong we made a short stop on the way back, just enough time to have a look at some plants that are flowering.

Starting with the least interesting, because invasive: Ageratina adenophora (Asteraceae), an introduced weed that was doing very well indeed all along the roadsides.

According to colleagues this is Eriostemon (Philotheca?) australasius (Rutaceae). The flowers are white; books usually show them as pink, but maybe the difference has something to do with this plant growing in shade. Very pretty, at any rate.

And finally we saw this even prettier orchid. After consulting Native Plants of the Sydney Region I presume it is Thelymitra ixioides, but orchids are not really my specialty.

Monday, September 18, 2017

Some quick, handy references

I just read that an Australian Senator called Fierravanti-Wells said the following:
I believe that marriage is between a man and a woman ... coming together in one unique union. That is what it has been for every culture, in every ethnicity, in every faith in every corner of the world for thousands and thousands of years.
Suggested reading:
The primary literature is cited in those entries. Also:
It would appear that the premise of this particular argument is demonstrably false. It would further appear that it is also not a logically valid argument, regardless of the truth or falseness of its premise:

Thursday, September 14, 2017

Botany picture #253: Coronidium waddelliae

Coronidium waddelliae (Asteraceae), Blue Mountains, 2016. This is very pretty perennial everlasting paper daisy that likes a bit of elevation. It can, for example, also be found in the lower parts of the Australian Alps.

Although only created in 2008 as part of the dismantling of the formerly polyphyletic Helichrysum, the genus Coronidium is unfortunately polyphyletic itself; the species that can be seen in an earlier post is a representative of the group that makes it so. What is more, even if that group were kicked out, the rest (to which C. waddelliae belongs) would still be paraphyletic to the well known golden everlasting genus Xerochrysum.

We are working on it.

Monday, September 11, 2017

What exactly is new about New Atheism?

On Sunday I went back to the book fair with my family, and of course I bought another few books. One of them is a collection of essays written by Bertrand Russell. As its title is Why I am not a Christian it is unsurprising that its first chapter is his talk of the same title, which he originally gave in 1927.

Summarising in order, the talk makes the following points:

He starts by giving his definition of Christian. For Russell this requires at a minimum belief in the existence of a god, in immortality, and that Jesus Christ was "the best and wisest of men".

Next, Russell disposes of several common arguments for the existence of God, observing along the way that the most frequently used arguments have become less respectable over time. The first cause argument falls flat the moment somebody asks "who made God?", because if God is allowed not to have an explanation then one could just as well allow the universe not to have an explanation.

The natural law argument does not work because it conflates human laws, which are prescriptive and indeed have law-givers, with natural laws, which are merely descriptive, merely scientific descriptions of what happens instead of prescriptions of what should happen. As such they do not need a law-giver. Russell also points out that science has shown them to be largely "statistical averages such as would emerge from the laws of chance; and that makes this whole business of natural law much less impressive than it formerly was." Finally he adds a Euthyphro style argument, that laws are not really laws if God just made them up, but that God is not required if they are truly laws of nature.

The argument from design was destroyed by Charles Darwin, and in that context Russell also introduces the argument from evil to show that the world does not look as if it was created by a benevolent, omnipotent being.

The moral argument is quickly disposed of by applying the Euthyphro dilemma.

Russell calls the argument for the remedying of injustice, i.e. the idea that god must exist or else there would be no ultimate justice in the world, very "curious", and I can only agree. I have only once seen it used in seriousness, and it is such blatant wishful thinking that it hardly needs refutation.

Having dealt with the existence of God, Russell transitions to the character of Christ. He calls "excellent" several of Jesus' teachings that I would consider unrealistic, for example 'turn the other cheek', but sarcastically points out that Christians do not actually follow those teachings. ("I have no doubt that the present Prime Minister, for instance, is a most sincere Christian, but I should not advise any of you to go and smite him on one cheek. I think you might find that he thought this text was intended in a figurative sense.")

As an aside, Russell mentions that "historically it is quite doubtful whether Christ ever existed at all".

More importantly, Russell says that there are "defects" in the teachings of Jesus the character of the gospels, most prominently that he mistakenly believed that the end of the world was imminent and that he believed in and took "a certain pleasure" in hell, i.e. eternal torture. The undeserved killing of a fig tree also gets a mention.

At this point Russell has explained why he is not a Christian. He now deals with the idea that even if religion is wrong it should still be promoted because it makes people behave morally by pointing out that it does the exact opposite. "You find as you look around the world that every single bit of progress in humane feeling, every improvement in the criminal law, every step towards the diminution of war, every step towards better treatment of the coloured races, or every mitigation of slavery, every moral progress that there has been in the world, has been consistently opposed by the organised Churches of the world."

The talk ends by arguing that fear of the unknown and of death is the foundation of religion, and that it is time to dispose of it and build a good world on a new foundation: "Science can help us to get over this craven fear in which mankind has lived for so many generations."


Russell was certainly an excellent writer, at least to my taste. He was concise, clear, and to the point. But really what struck me most when I read this talk / essay is that there really is no New to what has been called New Atheism these past fifteen years or so, i.e. the movement often considered personified by Richard Dawkins, Sam Harris, Daniel Dennett and Christopher Hitchens.

Because what really is its claim to novelty? Perhaps the first thing that comes to mind is the claim that religion is not just wrong but harmful, and that its influence should be reduced. But go back a few paragraphs and you will see that Russell said the same in 1927.

Another idea is that its novelty might be in the view that science in particular has made belief in gods untenable, a position that is often derided as 'scientism' by philosophers who believe that they have a monopoly on refuting religious beliefs. Again, nothing new: where today some New Atheist might argue from evolution, astrophysics and neuroscience, a hundred years ago an atheist like Russell argued from evolution and astrophysics. And to be honest, neuroscience has found nothing in the last thirty years that refutes the concept of an immaterial soul more thoroughly than what people could already observe in the bronze age, for example that a strike to the head or drinking alcohol confuses our thinking.

Even rather specific side-issues have remained surprisingly unchanged. Richard Carrier et al. have in recent years made a lot of waves with the argument that Jesus never existed, and would you not know it, ninety years ago Russell mentioned this idea in a tone that suggests it was fairly widely accepted among educated people.

Really I don't think that arguments for or against gods have made much progress since 1859, and if somebody wanted a short but reasonably thorough introduction to atheist thought they would even today be well served with reading Bertrand Russell's Why I am not a Christian.

Saturday, September 9, 2017

Book fair o'clock

It is the time of the Lifeline charity book fair again. Unfortunately I had to go alone today, but tomorrow we hope to get the whole family there. The loot so far:

Susanna Clarke, Jonathan Strange & Mr Norrell. Fantasy alternate history, as in the Napoleonic times with magic. I have read good things about this book, so I'm happy to give it a try.

Bertrand Russell's Best, edited by Rogert Egner

Terry Jones, Douglas Adam's Starship Titanic. If I understand correctly this is a book after a computer game with which I am not familiar.

Anne McCaffrey, Dragonflight. First novel of the Dragonriders of Pern series. The series has lots of volumes, and I could have bought more of them, but who knows how they are?

Anne McCaffrey, Dragonquest. Second novel in that series.

Kirk Mitchell, Cry Republic. As a teenager I read the trilogy of which this is the third novel in German translation. It is an alternate history story in which the Roman Empire never collapsed and has discovered electricity, steam and flight. Just noticed that the praise blurb on the front cover quotes Anne McCaffrey.

Great Dialogues of Plato, translated by W.H.D. Rouse. Continuing my education in classics, which perhaps should have happened in late high school but didn't.

Sean Williams, The Stone Mage and the Sea. I am afraid part of the reason I bought it is that I got confused and thought the author was Tad Williams. Ah well.

And for work:

H.T. Clifford & Gwen Ludlow, Keys to the Families and Genera of Queensland Flowering Plants. From the 1970s, but will still be useful.

Nicholas Gotelli, A Primer of Ecology. Having been trained as a systematist I am hoping to get a bit more insight into ecological modeling, and it includes a chapter on island biogeography that looks promising.

Andrew Young & Geoffrey Clarke, Genetics, Demography and Viability of Fragmented Populations. Because of a project I am currently involved with.

Two observations. First, as always I come home with loads of books but could only bring myself to donating two. Some day we will have to expand our book shelves, and I have no idea where. Second, it is astonishing how there are numerous copies of some books (e.g. McCaffrey's Nerilka's Story) but none whatsoever of other, one would think, equivalent books (e.g. the third volume of the same series).

Also, are the frequent ones frequent because they were so much more popular when they were published, or because nobody wants them now? On that note, it was interesting to see that the most frequent book in the "all faiths" section was The God Delusion. It was all the rage a decade ago, and I assume now lots of people think they don't need it anymore.

Tuesday, September 5, 2017

Botany picture #252: Stapelia

With spring in the air we bought some plants lately, including some succulents, and that brought my mind back to some of the plants I had in Europe but gave away when moving to Australia. This is a Stapelia, presumably S. grandiflora (Apocynaceae), in the Old Botanic Garden of Göttingen, Germany, 2016. I had a plant of the same species but of course much smaller.

Unfortunately they seem to be hard to get in Australia. The closest I saw were online stores that had them in the catalogue in theory but not actually in stock.

What is so amazing about these cactus-like plants that are not cacti at all is, of course, their flower morphology, and that morphology is dictated by their pollination ecology. The flowers mimic rotting meat in colour, scent and sometimes even hairiness and are pollinated by confused carrion flies. Some people wonder why one would want to have a stinking flower, but I believe that is an indispensable part of its wonderful weirdness.

Saturday, September 2, 2017

Having fun with biodiversity databases

If you have ever professionally used a biodiversity database you will soon have noticed that we still have a long way to go before they are as reliable as we would like them to be.

Today I looked into the Atlas of Living Australia records for Senecio australis (Asteraceae). Except for a rather odd specimen from South Africa the distribution records look like this:

What do we have here? First, the four Australian mainland records all appear to be misapplications of the name. The Flora of New South Wales, for example, does not even mention the species, so I think we can safely assume it does not occur in Australia at all.

Second, the record in the middle of the top of the map is right in the ocean, no matter how closely we zoom in. If we look into its details, we see that it was collected on Norfolk Island, which is the cluster of red dots to its right, so somebody must have got the coordinates rather wrong.

Third, there is a cluster around Auckland, on New Zealand's North Island. I am not sure if Norfolk Island and North Island is a plausible area of distribution for this species, but it may well be. Zooming in closer to Norfolk Island, however, ...

... it looks as if somebody had played darts after having had a few too many beers. ALA informs us dryly under the section data quality tests, "habitat incorrect for species". No kidding. Or as my wife joked, unwilling to believe that the coordinates would be so badly off for such a large percentage of the specimens, "is there a fish that is also called Senecio australis?"

These are the problems that we are dealing with, more generally.
  • Whenever we do a study using data from biodiversity databases, as we increasingly do, we have to be very careful about cleaning the data. The main issues are outdated taxonomy, misidentifications, spatial data entry errors (which are particularly easy to recognise if an outlier record is exactly ten degrees away from a known occurrence), and imprecise spatial data. Just think of what it would do to species distribution modeling if we uncritically accepted all the records for Senecio australis.
  • While we can identify obvious mistakes while using a database, the data are "ground-truthed" in the actual specimens in some herbarium or museum, and the policy is usually (and quite sensibly) that the database won't update until a correction is made to that specimen in its home institution and then filters through from there. But many institutions do not have the resources to update data just because somebody sent them an eMail pointing out that their specimen is misidentified or that they made a data entry error; many herbaria on the planet are so understaffed that even the word understaffed is a euphemism. What is more, even if a database allows a registered user to annotate a record with corrections, the information may not necessarily flow back to the institution holding it, depending on whether somebody thought to set up such procedures or not.
  • Overall, Australia actually has excellent data quality, the Atlas of Living Australia actually allows annotations to be made, and several important Australian herbaria actually have the staffing to update their data. What I am saying is that this is as good as you can have it at the moment. It is much more difficult in many other parts of the world, and of course it would be good if we could have the same or better data quality for those areas.
Also, perhaps it is best not think too much about records that are not specimen-based but "human observations" or photos submitted by random people. There are, obviously, non-taxonomists whose knowledge of the flora is extensive, and citizen science can be awesome, but I have also seen several cases one the lines of "aaargh ... this is so misidentified it is not even the right tribe of the family, and now the database is using it as the profile picture of this nationally significant weed species!"

Wednesday, August 30, 2017

Botany picture #251: Schizaea bifida

I have been meaning to post something more substantive, but very busy with other things. So here another plant, and a strangely looking one: Schizaea bifida (Schizaeaceae), a little fern from the Blue Mountains, 2011. Yes, except for the rootstock that is it, that's the whole fern. Some species of Schizaea have finely divided sterile leaves, but as the Flora of NSW Online remarks, in this species they are "rarely present", so what you see is a cluster of green lines with sporangia on top, the fertile leaves in all their splendour. But who is complaining? I love weird plants.

This was one of the plant groups I had only read about before coming to Australia, so when I saw it during a family holiday I was very happy. Sadly I have not again run into the genus since that one time six years ago.

Friday, August 25, 2017

Phylogenetic trees in XML format

I recently had the extremely frustrating experience of having had to look into how phylogenetic trees are coded in XML format. To illustrate why this was frustrating, let us start by considering a small phylogenetic tree as an example. I got one sequence each for the genera Nassauvia, Erigeron, Xerochrysum, Matricaria, Lactuca, Senecio, Ursinia, Calycera, Kippistia, and Synedrella from Genbank, and produced a likelihood tree in PAUP. In graphical representation it looks as follows.

So how is it generally saved? The most concise way of scoring a phylogenetic tree in plain text files is the venerable and widely accepted Newick standard. It consists of OTU names separated by commas and grouped into clades by round brackets. There may be numbers after colons, which are branch lengths, and if there is a number directly after a closing bracket it indicates some kind of support value, such as bootstrap or Bayesian posterior probability. The Newick representation of my little example tree is as follows.

Again, very concise. If we want just a tiny bit more bells and whistles we can use the Nexus format. In the context of phylogenetic trees it is just the Newick format plus "#nexus [line break] begin trees;" at the beginning and "end;" after the trees, and then each Newick tree has "tree [name of tree] =" in front of it and another semicolon at the end. The main advantage is that multiple trees in the same file can now have informative names, whereas in a Newick file they cannot.

If we want to find out how this would look in XML format, we can head over to the website, where we will find an online tool that can transform our boring old Newick or Nexus trees into shiny, exciting, newfangled NeXML trees (for Nexus-inspired XML I guess, although as we will soon see there isn't really any similarity at all). Of course for this post I have done that with the example tree.

So, what do we see? As the name XML implies, the format is similar to HTML in that it consists largely of nested sets of tags starting with is-smaller-than signs and ending with is-larger-than signs. But those are just the optics. What about functionality?

As a Newick file, my phylogenetic tree was 448 bytes in size. After transformation into NeXML, the new tree file is now 2645 bytes in size, an increase by 490%. This has several obvious benefits in particular for the results of Bayesian analyses where thousands of trees have to be saved and may take up megabytes even in Newick format, for example I can't think of any right now.

And I am not even going to go into how NeXML scores data matrices beyond observing that it appears to require a tag assigning character type for every individual character. In other words, instead of saying something like "characters 1-9000 are anonymous genome-wide SNPs with the possible states 0, 1, 2 and ?", as in Nexus files, you would have 9000 lines of code (!) each saying "character 4306 is a SNP character" and then "character 4307 is a SNP character", and so on, wasting enormous amounts of disk space and/or bandwidth. Efficiency!

More generally, the structure of the tree coded as NeXML is extremely convoluted compared to what it looks like in Newick format. Newick is, as mentioned above, a set of nested brackets indicating clades; consequently it can be examined and read relatively easily, and even allows the user to copy subtrees in or out in manual editing (it helps if you have a text editor like SciTE that shows which brackets belong together). In fact I have often produced hypothetical example trees to illustrate a point on this blog by typing them out in Newick format and then opening them in a tree viewer. NeXML, however, has a list of nodes and edges that are referring to each other via obscure identifiers, making it virtually impossible to read, type out and edit manually, especially for larger trees. But I am sure XML makes life easier for the end user because please insert reasons here.

Next, imagine writing a program that should be able to read a phylogeny. If you want it to read a Newick tree, you merely need to parse nested brackets, recognise taxon names, and deal with branch length and support value annotations; this is relatively straightforward. If you want it to be able to read NeXML trees, on the other hand, it needs to be able to handle a large number of possible tags in varying order, plus various parameters in each tag that can appear in varying order (<node id="ne16" otu="ou27" label="Senecio_vulgaris"/> could just as well be <node otu="ou27" label="Senecio_vulgaris" id="ne16"/>, for example). This makes life easier for programmers because I'm sorry I really have no idea. But I mean, the website says that this format is "more easily validated and processed", so that must be true, right? Otherwise they wouldn't claim so, would they?

While on the topic of phylogenetics software, to the best of my knowledge none of the programs that I currently use or have seriously used in the past can read or write phylogenies in XML format. BEAST, PAUP, and MrBayes produce Nexus files, TNT exports its own idiosyncratic format or Nexus, and RAxML produces Newick files. (BEAST uses famously convoluted XML input files, but even here the assumption is that most users import Nexus data matrices into the GUI BEAUTi. At any rate it does not save its output as NeXML.) Mesquite, which uses Nexus as its default format, is supposed to be able to export into NeXML format once we install a certain add-on library, but when I tried to do such a conversion I merely got an incomprehensible crash report.

Perhaps more to the point, if NeXML phylogenies produced by some obscure phylogenetics software that I never employ myself are supposed to be of use they have to be displayed, so how are we doing for tree viewers? The very popular cross-platform software FigTree expects Nexus or Newick phylogenies, and as far as I know the same is true for TreeView. DendroScope claims to read NeXML files but then only gave me an error message when I tried to import the simple example phylogeny after conversion by the official website. To quote from that same website, "the future data exchange standard is here!"

While on that topic, standardisation is one of the main benefits claimed by NeXML or by XML more generally. As Simon St. Laurent wrote already in 1998:
XML allows developers to set standards defining the information that should appear in a document, and in what sequence. XML, in combination with other standards, makes it possible to define the content of a document separately from its formatting, making it easy to reuse that content in other applications or for other presentation environments. Most important, XML provides a basic syntax that can be used to share information between different kinds of computers, different applications, and different organizations without needing to pass through many layers of conversion.
I guess at this stage it should come as no surprise at all that there are already at least two different XML standards for phylogenetic trees, which is another way of saying that there is no XML standard for phylogenetic trees. In addition to NeXML, which I have discussed in detail above, there is phyloXML. Where NeXML describes trees using lists of nodes and edges phyloXML uses nested clade tags, which I find more intuitive and useful because it allows easier parsing and easier manual editing, and which is also more similar in spirit to Newick and Nexus and would thus be more deserving of a name like NeXML than NeXML. Otherwise it appears to be just as inefficient and convoluted though.

So concerning standardisation I guess the reality is that XML is flexible enough that anybody could come up with a new, XML-based standard. Just think of a few words, put is-smaller-than and is-larger-than signs around them, convince a handful of colleagues to adopt this standard, and off you go. Yes, if it is so easy to do then everybody will do it, and then we achieve the exact opposite of standardisation, but I guess that is where XML proponents can switch to touting its "flexibility". Heads XML wins, tails all other data standards lose.

As far as I can see Newick and Nexus work just fine. Compared to XML phylogenies they are easier to parse, are already standardised, are accepted by virtually every phylogenetics software and tree viewer, and take up a fraction of the disk space. Why fix what isn't broken?

Sunday, August 20, 2017

I still don't get area cladistics, and 'geographic paralogy' in particular

Since I started looking into panbiogeography and area cladistics, I have been curious about the concept of geographic paralogy. The word is used by area cladists (in the widest sense), and I have so far been doubtful about whether the analogy to gene paralogy fits.

To recap, area cladistics attempts to infer biogeographic area relationships from the patterns that species' areas of distribution show on a phylogenetic tree. If, for example, several plant or animal groups show distributions on a phylogeny that are ( Africa, ( South America , Australia ) ), i.e. sister lineages are endemic to South America and Australia, and more distantly related lineages are endemic to Africa, then an area cladist would conclude that South America and Australia are "more closely related" biogeographically than either is to Africa, or even that they form a "monophyletic biogeographic area".

Whatever that is supposed to mean, given that the word monophyletic only applies if we presuppose tree-like relationships. But I am getting ahead of myself.

The problem is now that phylogenies do not necessarily show such a simple pattern. Some species may be widespread and occur in several of the areas in the analysis, and of course the same area may occur repeatedly in different parts of the phylogeny. This is what area cladists call 'geographic paralogy', and they 'solve' the problem it poses for their analyses by selecting 'paralogy-free' subtrees from a phylogeny.

Again, two questions: Does it make sense to call this geographic paralogy, in analogy to gene paralogy? And does it make sense to do area cladistics by cherry-picking 'paralogy-free' subtrees, effectively ignoring these patterns?

I started a conversation with a colleague at the IBC, and he recommended I read Ladiges (1998, "Biogeography after Burbidge", Australian Systematic Botany 11: 231-242) as an introduction to the relevant concepts and approaches. So this I have now done. Unfortunately, the paper did not really solve my conceptual problems. I will start with a few quotes:
In cladistic biogeography, nodes of a cladogram for organisms (1,2 and 3) are potentially informative about the geographic areas (A, B and C) in which they occur: node 2 in Fig. 3 shows that areas B and C are related more closely to each other than to area A.

Such statements of relationship, the nodes of the cladogram, are explained by a variety of historical theories. One is dispersal from a restricted ancestral area, for example from area A to areas B and C, a pattern that may match fossil ages and distribution. An alternative explanation is vicariance of a widespread ancestral species coincident with physical breakup or climatic differentiation of the general area. A vicariance explanation is favoured by evidence of biogeographic congruence: finding the same pattern for other groups of organisms.
So far so good, although I do wonder whether the concept of area relationships makes sense if dispersal is the right answer. It seems to me that even calling it relationships only makes sense if there is no frequent floristic or faunal exchange, if near-everything is due to vicariance. And as I have mentioned before, there are good alternative explanations for congruence that do not imply vicariance, in particular prevailing directions of wind or ocean currents, common routes of migratory birds, etc.

Now come the complications:
Data for any one group of organisms are rarely as simple as the example shown (...). Some taxa are widespread, and some areas have more than one taxon. When combining data for different groups of organisms, not all areas are represented in each taxonomic group. Such complications are obstacles to development of analytical methods for determining area cladograms and general area cladograms.
Well yes, either that or, alternatively, they prove that the concept of an area cladogram is as incoherent as a 'species-level phylogeny' with only human populations as the terminals, and that the research program of area cladistics is a non-starter. Two pages on, the term at the centre of this post is introduced.
I offer two conclusions: (1) that evidence of historical geographic relationship is associated with nodes (not the distribution per se of terminal taxa) and (2) that some nodes of cladograms of organisms are paralogous. (...)

What is geographic paralogy? It is evidenced by duplication or overlap in geographic distribution of taxa related at a node (references). The term has its origin in molecular biology, geographic paralogy being analogous to gene duplication, with each gene copy subsequently tracking a separate evolutionary history.

(...) There is duplication of biogeographic regions across the clades (e.g. South America is in three), which is evidence of geographic paralogy. In other words, the major lineages shown in the cladogram existed prior to the breakup of Gondwana and each potentially reflects that geological history.
Consider what is claimed here. First, as we have seen earlier, simple area relationships that are congruent across lineages are claimed as evidence for vicariance. Now the fact that the same area shows up in several parts of a phylogeny is seen as evidence for paralogy; and this paralogy is also seen as evidence for vicariance and against dispersal. I cannot say that this makes a lot of sense to me.

Having gone through these quotes, I now want to carefully examine the analogy between gene paralogy and geographic paralogy. Let's start with the former. It works like this:

In this and the following figures, we see a grey species tree with species 1, 2 and 3. Within it we see the gene trees, as genes evolve inside the species. Here an originally single gene lineage (blue) was duplicated in the common ancestor of all three species, creating a red gene and a black gene. We now call the alleles A and Y paralogues of each other, because while they are distantly related they are not really the same gene anymore. In contrast, A and B are orthologues of each other. They are really the same gene, only in two different species.

The above figure now shows the problem that gene paralogy can cause in phylogeny reconstruction. If in this case Z is wrongly assumed to be an orthologue of A and B, we will infer the wrong species relationships, i.e. ((1,2),3) instead of the true (1,(2,3)). However, there are also other causes why we may get conflicting or complicated patterns.

In the above case we have the gene tree contradicting the species tree, but nonetheless there is no paralogy because there is only one gene involved. What has happened here is that two versions of the gene arose in an ancestral population, and that subsequent populations were large enough and/or speciation events happened so close after each other that both copies were carried through to the ancestor of 2 and 3. We call this incomplete lineage sorting (ILS) or ancestral polymorphism. We could also still find all gene variants in all three species. Point is, this is not paralogy.

Something different has happened in the above scenario. We get the same pattern of a gene tree showing ((1,2),3) despite the species phylogeny of (1,(2,3)), but this time because of a hybridisation or introgression event between 1 and 2. Of course, we could also still find the original gene variant in species 2 along with the introgressed one. Again, this is not paralogy.

Now the same for biogeography. Above the scenario where I think the analogy works: There are two clades that arose before continental breakup, and they both independently trace the 'area relationships'. In this case it makes sense to use the two clades or subtrees as independent data points for inference in area cladistics.

Here is the same problem for area cladistics as for phylogenetic inference. If we do not realise that we are treating paralogues as orthologues, we may get species phylogenies and, by analogy, area relationships wrong. So in the case of phylogenetics, people have developed methods for orthologue inference and to exclude paralogues from the data.

What I don't really see is how area cladists do the same. They claim they pick 'paralogue-free subtrees', but that merely means that they search for a statement like ((1,2),3) and remove statements like (1&2&3,(1&2,2&3)). It does  not mean that they actually have any way of recognising that ((1,2),3) is an instance of paralogy while (1,(2,3)) isn't. They can merely hope that it comes out in the wash because the true relationship will be more frequent than the wrong ones.

This appears to be rather problematic, unless I am missing something equivalent to orthology inference in phylogenetics. But on top of that we have the other scenarios, those where there really is no paralogy.

The above is the biogeographic equivalent of incomplete lineage sorting. We could imagine here that species C stayed endemic to a part of South America while its sister species was more widespread. If we now also had some species occurring in two areas, area cladists would speak of paralogous nodes, but again, there does not appear to be any paralogy involved.

But really crucial is the biogeographic parallel to gene introgression: dispersal. The above scenario shows what area cladists call paralogy and, as we saw in the quotes above, consider evidence of vicariance, but what reason is there to exclude dispersal as a possible explanation? This is, of course, precisely the pattern that dispersal would produce!

And it is clearly not in any way comparable to gene paralogy anyway, because there are no paralogues involved. It makes no sense to use a term that assumes the existence of two genes independently tracing the species phylogeny (and, by analogy, two species-lineages independently tracing 'area relationships') to refer to any difficult pattern, even where there are no such two deep species-lineages.

In summary, I am still not exactly convinced that area cladistics makes sense. The assumption that pretty much any pattern - congruence as well as the contradictory data from paralogy! - is evidence of vicariance seems particularly hard to swallow.